Starting phenix.real_space_refine on Thu Feb 5 02:52:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dfv_46819/02_2026/9dfv_46819.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dfv_46819/02_2026/9dfv_46819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dfv_46819/02_2026/9dfv_46819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dfv_46819/02_2026/9dfv_46819.map" model { file = "/net/cci-nas-00/data/ceres_data/9dfv_46819/02_2026/9dfv_46819.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dfv_46819/02_2026/9dfv_46819.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.039 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 97 5.16 5 C 8990 2.51 5 N 2433 2.21 5 O 2715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s 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: 14247 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2911 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2951 Chain: "C" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 5390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5390 Classifications: {'peptide': 670} Link IDs: {'PTRANS': 26, 'TRANS': 643} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AVAL B 45 " occ=0.51 ... (12 atoms not shown) pdb=" CG2BVAL B 45 " occ=0.49 residue: pdb=" N AGLY B 46 " occ=0.51 ... (6 atoms not shown) pdb=" O BGLY B 46 " occ=0.49 Time building chain proxies: 4.21, per 1000 atoms: 0.30 Number of scatterers: 14247 At special positions: 0 Unit cell: (91.8, 159.84, 139.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 97 16.00 P 8 15.00 Mg 4 11.99 O 2715 8.00 N 2433 7.00 C 8990 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: 1.39 Conformation dependent library (CDL) restraints added in 642.8 milliseconds 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3334 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 24 sheets defined 51.1% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.713A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.861A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.946A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.699A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.553A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.654A pdb=" N CYS A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.137A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 350 through 355 removed outlier: 4.232A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.962A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.827A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.883A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 removed outlier: 3.536A pdb=" N ILE B 267 " --> pdb=" O PRO B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.552A pdb=" N CYS B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.301A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.698A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.732A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.629A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.648A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.108A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 205 through 217 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.521A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.929A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.529A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.962A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.169A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 60 through 65 Processing helix chain 'D' and resid 69 through 73 Processing helix chain 'D' and resid 77 through 91 Processing helix chain 'D' and resid 115 through 123 Processing helix chain 'D' and resid 133 through 149 removed outlier: 3.632A pdb=" N ILE D 137 " --> pdb=" O HIS D 133 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS D 146 " --> pdb=" O TYR D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 179 removed outlier: 3.708A pdb=" N SER D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 200 removed outlier: 4.455A pdb=" N GLN D 187 " --> pdb=" O SER D 183 " (cutoff:3.500A) Proline residue: D 194 - end of helix Processing helix chain 'D' and resid 239 through 243 removed outlier: 3.505A pdb=" N CYS D 243 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 260 removed outlier: 4.202A pdb=" N TYR D 256 " --> pdb=" O TYR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 271 Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 308 Processing helix chain 'D' and resid 311 through 330 Processing helix chain 'D' and resid 349 through 360 removed outlier: 3.807A pdb=" N ALA D 353 " --> pdb=" O SER D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 371 Processing helix chain 'D' and resid 387 through 419 removed outlier: 3.635A pdb=" N ALA D 417 " --> pdb=" O LYS D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 473 removed outlier: 3.545A pdb=" N HIS D 460 " --> pdb=" O PHE D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 482 removed outlier: 4.210A pdb=" N SER D 481 " --> pdb=" O TYR D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 500 Processing helix chain 'D' and resid 505 through 516 removed outlier: 3.589A pdb=" N LYS D 515 " --> pdb=" O ASP D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 533 Processing helix chain 'D' and resid 574 through 584 removed outlier: 3.885A pdb=" N ILE D 578 " --> pdb=" O HIS D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 593 removed outlier: 3.632A pdb=" N LYS D 590 " --> pdb=" O ASN D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 606 removed outlier: 3.871A pdb=" N LYS D 605 " --> pdb=" O GLU D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 628 removed outlier: 3.620A pdb=" N CYS D 628 " --> pdb=" O THR D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 660 removed outlier: 3.807A pdb=" N GLY D 660 " --> pdb=" O LEU D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 671 removed outlier: 3.867A pdb=" N ILE D 665 " --> pdb=" O MET D 661 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 4.004A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.785A pdb=" N GLN A 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.785A pdb=" N GLN A 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA7, first strand: chain 'A' and resid 169 through 170 removed outlier: 5.938A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA9, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.478A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.503A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.229A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 26 through 27 Processing sheet with id=AC2, first strand: chain 'D' and resid 95 through 97 removed outlier: 6.213A pdb=" N LEU D 102 " --> pdb=" O ARG D 634 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE D 636 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA D 104 " --> pdb=" O ILE D 636 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY D 158 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 433 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE D 219 " --> pdb=" O ILE D 433 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 201 through 202 Processing sheet with id=AC4, first strand: chain 'D' and resid 333 through 336 Processing sheet with id=AC5, first strand: chain 'D' and resid 372 through 374 Processing sheet with id=AC6, first strand: chain 'D' and resid 538 through 539 700 hydrogen bonds defined for protein. 1884 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: 2.71 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4676 1.34 - 1.46: 3227 1.46 - 1.58: 6477 1.58 - 1.70: 12 1.70 - 1.82: 165 Bond restraints: 14557 Sorted by residual: bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.07e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.98e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.70e+00 bond pdb=" CG HIC C 73 " pdb=" CD2 HIC C 73 " ideal model delta sigma weight residual 1.369 1.411 -0.042 2.00e-02 2.50e+03 4.49e+00 bond pdb=" CG HIC A 73 " pdb=" CD2 HIC A 73 " ideal model delta sigma weight residual 1.369 1.411 -0.042 2.00e-02 2.50e+03 4.46e+00 ... (remaining 14552 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 19194 1.61 - 3.22: 438 3.22 - 4.83: 60 4.83 - 6.44: 33 6.44 - 8.05: 5 Bond angle restraints: 19730 Sorted by residual: angle pdb=" N GLY D 261 " pdb=" CA GLY D 261 " pdb=" C GLY D 261 " ideal model delta sigma weight residual 116.01 107.96 8.05 1.64e+00 3.72e-01 2.41e+01 angle pdb=" N GLY B 55 " pdb=" CA GLY B 55 " pdb=" C GLY B 55 " ideal model delta sigma weight residual 111.35 116.54 -5.19 1.20e+00 6.94e-01 1.87e+01 angle pdb=" C ALA D 38 " pdb=" N VAL D 39 " pdb=" CA VAL D 39 " ideal model delta sigma weight residual 121.97 129.74 -7.77 1.80e+00 3.09e-01 1.86e+01 angle pdb=" N GLU D 567 " pdb=" CA GLU D 567 " pdb=" C GLU D 567 " ideal model delta sigma weight residual 113.43 108.43 5.00 1.26e+00 6.30e-01 1.57e+01 angle pdb=" N VAL C 201 " pdb=" CA VAL C 201 " pdb=" C VAL C 201 " ideal model delta sigma weight residual 113.53 110.25 3.28 9.80e-01 1.04e+00 1.12e+01 ... (remaining 19725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.17: 8561 27.17 - 54.33: 175 54.33 - 81.50: 28 81.50 - 108.67: 3 108.67 - 135.84: 4 Dihedral angle restraints: 8771 sinusoidal: 3579 harmonic: 5192 Sorted by residual: dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 164.16 135.84 1 2.00e+01 2.50e-03 4.12e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 69.47 -129.47 1 2.00e+01 2.50e-03 3.93e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 67.59 -127.60 1 2.00e+01 2.50e-03 3.86e+01 ... (remaining 8768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1916 0.066 - 0.132: 249 0.132 - 0.198: 4 0.198 - 0.263: 1 0.263 - 0.329: 1 Chirality restraints: 2171 Sorted by residual: chirality pdb=" CB VAL D 39 " pdb=" CA VAL D 39 " pdb=" CG1 VAL D 39 " pdb=" CG2 VAL D 39 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB ILE D 454 " pdb=" CA ILE D 454 " pdb=" CG1 ILE D 454 " pdb=" CG2 ILE D 454 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE D 227 " pdb=" CA ILE D 227 " pdb=" CG1 ILE D 227 " pdb=" CG2 ILE D 227 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 2168 not shown) Planarity restraints: 2541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 47 " -0.023 2.00e-02 2.50e+03 1.90e-02 8.99e+00 pdb=" CG TRP D 47 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP D 47 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP D 47 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 47 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 47 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 47 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 47 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 47 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 47 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 439 " 0.014 2.00e-02 2.50e+03 1.56e-02 4.26e+00 pdb=" CG PHE D 439 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE D 439 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE D 439 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE D 439 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE D 439 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 439 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG D 502 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO D 503 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 503 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 503 " 0.028 5.00e-02 4.00e+02 ... (remaining 2538 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 89 2.58 - 3.16: 11602 3.16 - 3.74: 21871 3.74 - 4.32: 31441 4.32 - 4.90: 52536 Nonbonded interactions: 117539 Sorted by model distance: nonbonded pdb=" OG1 THR D 165 " pdb="MG MG D 701 " model vdw 1.995 2.170 nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 2.040 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.056 2.170 nonbonded pdb=" OE1 GLN D 474 " pdb=" OH TYR D 477 " model vdw 2.064 3.040 nonbonded pdb=" O GLY C 156 " pdb=" OG1 THR C 303 " model vdw 2.128 3.040 ... (remaining 117534 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 5 through 44 or resid 47 through 402)) selection = (chain 'B' and (resid 5 through 44 or resid 47 through 402)) selection = (chain 'C' and (resid 5 through 44 or resid 47 through 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 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: 10.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.920 Find NCS groups from input model: 0.180 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.003 0.057 14557 Z= 0.139 Angle : 0.610 8.051 19730 Z= 0.320 Chirality : 0.043 0.329 2171 Planarity : 0.004 0.051 2541 Dihedral : 12.040 135.836 5437 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.16 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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: 0.31 (0.20), residues: 1774 helix: 0.86 (0.19), residues: 761 sheet: -0.01 (0.29), residues: 300 loop : -0.27 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.022 0.001 TYR D 9 PHE 0.036 0.001 PHE D 439 TRP 0.051 0.002 TRP D 47 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00280 (14557) covalent geometry : angle 0.60956 (19730) hydrogen bonds : bond 0.20123 ( 693) hydrogen bonds : angle 6.76291 ( 1884) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASP cc_start: 0.7797 (m-30) cc_final: 0.7498 (m-30) REVERT: B 82 MET cc_start: 0.8361 (tpt) cc_final: 0.8093 (tpt) REVERT: B 326 LYS cc_start: 0.8354 (mttp) cc_final: 0.7941 (mmtm) REVERT: C 360 GLN cc_start: 0.8419 (tp40) cc_final: 0.7382 (tp40) REVERT: D 65 HIS cc_start: 0.7387 (m90) cc_final: 0.6983 (m90) REVERT: D 120 ARG cc_start: 0.8617 (ptm-80) cc_final: 0.8232 (ptp90) REVERT: D 135 PHE cc_start: 0.8216 (m-10) cc_final: 0.7887 (m-80) REVERT: D 143 PHE cc_start: 0.8008 (t80) cc_final: 0.7729 (t80) REVERT: D 147 ARG cc_start: 0.7716 (tmm160) cc_final: 0.7351 (ttt-90) REVERT: D 159 GLU cc_start: 0.7803 (tp30) cc_final: 0.7369 (tt0) REVERT: D 178 ILE cc_start: 0.8193 (tp) cc_final: 0.7947 (tt) REVERT: D 262 MET cc_start: 0.6030 (ttm) cc_final: 0.5353 (ttm) REVERT: D 266 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7327 (mt-10) REVERT: D 422 PRO cc_start: 0.4388 (Cg_endo) cc_final: 0.4109 (Cg_exo) REVERT: D 442 GLU cc_start: 0.8321 (pm20) cc_final: 0.8115 (pm20) REVERT: D 546 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7262 (mt-10) REVERT: D 641 PHE cc_start: 0.7520 (m-80) cc_final: 0.7295 (m-80) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1409 time to fit residues: 42.8512 Evaluate side-chains 135 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN C 353 GLN D 35 GLN ** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN D 263 ASN D 279 ASN D 458 ASN D 463 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.102570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.076906 restraints weight = 47132.906| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.00 r_work: 0.2739 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14557 Z= 0.209 Angle : 0.638 8.817 19730 Z= 0.322 Chirality : 0.046 0.226 2171 Planarity : 0.005 0.065 2541 Dihedral : 9.041 138.045 1999 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.39 % Favored : 96.50 % Rotamer: Outliers : 0.72 % Allowed : 4.56 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.20), residues: 1774 helix: 0.76 (0.19), residues: 798 sheet: 0.18 (0.29), residues: 294 loop : -0.42 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 372 TYR 0.012 0.001 TYR B 143 PHE 0.015 0.002 PHE B 266 TRP 0.018 0.002 TRP B 79 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00500 (14557) covalent geometry : angle 0.63773 (19730) hydrogen bonds : bond 0.04763 ( 693) hydrogen bonds : angle 5.09518 ( 1884) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 123 MET cc_start: 0.9071 (mmp) cc_final: 0.8814 (mmp) REVERT: B 25 ASP cc_start: 0.8161 (m-30) cc_final: 0.7900 (m-30) REVERT: B 113 LYS cc_start: 0.8534 (mttt) cc_final: 0.8119 (mmtt) REVERT: B 221 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8545 (tp) REVERT: B 348 SER cc_start: 0.8969 (m) cc_final: 0.8688 (p) REVERT: C 360 GLN cc_start: 0.8438 (tp40) cc_final: 0.8195 (tp40) REVERT: D 41 ASP cc_start: 0.8726 (m-30) cc_final: 0.8282 (m-30) REVERT: D 65 HIS cc_start: 0.7150 (m90) cc_final: 0.6896 (m90) REVERT: D 120 ARG cc_start: 0.8554 (ptm-80) cc_final: 0.8188 (ptp90) REVERT: D 135 PHE cc_start: 0.8637 (m-10) cc_final: 0.8430 (m-80) REVERT: D 143 PHE cc_start: 0.8200 (t80) cc_final: 0.7920 (t80) REVERT: D 147 ARG cc_start: 0.7873 (tmm160) cc_final: 0.7557 (ttt-90) REVERT: D 159 GLU cc_start: 0.8157 (tp30) cc_final: 0.7813 (tt0) REVERT: D 178 ILE cc_start: 0.8185 (tp) cc_final: 0.7937 (tt) REVERT: D 191 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8279 (mm-30) REVERT: D 422 PRO cc_start: 0.4526 (Cg_endo) cc_final: 0.4268 (Cg_exo) REVERT: D 504 MET cc_start: 0.8704 (mmt) cc_final: 0.8195 (mmt) REVERT: D 546 GLU cc_start: 0.8505 (mm-30) cc_final: 0.7961 (mt-10) REVERT: D 641 PHE cc_start: 0.7864 (m-80) cc_final: 0.7654 (m-80) outliers start: 11 outliers final: 8 residues processed: 160 average time/residue: 0.1183 time to fit residues: 28.6460 Evaluate side-chains 142 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 477 TYR Chi-restraints excluded: chain D residue 581 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 GLN ** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.076631 restraints weight = 47576.677| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.03 r_work: 0.2732 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14557 Z= 0.170 Angle : 0.594 7.152 19730 Z= 0.297 Chirality : 0.045 0.222 2171 Planarity : 0.004 0.062 2541 Dihedral : 8.898 137.648 1999 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.16 % Favored : 96.72 % Rotamer: Outliers : 1.04 % Allowed : 6.58 % Favored : 92.37 % 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: 0.35 (0.20), residues: 1774 helix: 0.87 (0.19), residues: 797 sheet: 0.30 (0.30), residues: 294 loop : -0.45 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 372 TYR 0.012 0.001 TYR D 216 PHE 0.012 0.001 PHE B 266 TRP 0.017 0.002 TRP B 79 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00405 (14557) covalent geometry : angle 0.59358 (19730) hydrogen bonds : bond 0.04046 ( 693) hydrogen bonds : angle 4.78743 ( 1884) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 ASP cc_start: 0.8151 (m-30) cc_final: 0.7890 (m-30) REVERT: B 348 SER cc_start: 0.8908 (m) cc_final: 0.8613 (p) REVERT: C 360 GLN cc_start: 0.8550 (tp40) cc_final: 0.8065 (tp40) REVERT: D 41 ASP cc_start: 0.8738 (m-30) cc_final: 0.8294 (m-30) REVERT: D 65 HIS cc_start: 0.7263 (m90) cc_final: 0.6935 (m90) REVERT: D 120 ARG cc_start: 0.8618 (ptm-80) cc_final: 0.8205 (ptp90) REVERT: D 147 ARG cc_start: 0.7839 (tmm160) cc_final: 0.7582 (ttt-90) REVERT: D 178 ILE cc_start: 0.8230 (tp) cc_final: 0.8016 (tt) REVERT: D 191 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8135 (mm-30) REVERT: D 422 PRO cc_start: 0.4638 (Cg_endo) cc_final: 0.4389 (Cg_exo) REVERT: D 504 MET cc_start: 0.8694 (mmt) cc_final: 0.8480 (mmt) REVERT: D 546 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8079 (mt-10) REVERT: D 641 PHE cc_start: 0.7878 (m-80) cc_final: 0.7616 (m-80) outliers start: 16 outliers final: 10 residues processed: 150 average time/residue: 0.1126 time to fit residues: 26.4620 Evaluate side-chains 137 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 477 TYR Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 175 optimal weight: 8.9990 chunk 165 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.077766 restraints weight = 44630.946| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.94 r_work: 0.2754 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14557 Z= 0.126 Angle : 0.554 6.973 19730 Z= 0.274 Chirality : 0.043 0.240 2171 Planarity : 0.004 0.059 2541 Dihedral : 8.752 139.740 1999 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.11 % Favored : 96.78 % Rotamer: Outliers : 0.65 % Allowed : 8.08 % Favored : 91.26 % 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: 0.51 (0.20), residues: 1774 helix: 1.02 (0.19), residues: 805 sheet: 0.36 (0.29), residues: 292 loop : -0.39 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 95 TYR 0.009 0.001 TYR B 143 PHE 0.010 0.001 PHE D 221 TRP 0.020 0.002 TRP D 184 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00293 (14557) covalent geometry : angle 0.55382 (19730) hydrogen bonds : bond 0.03397 ( 693) hydrogen bonds : angle 4.60559 ( 1884) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: B 25 ASP cc_start: 0.8169 (m-30) cc_final: 0.7921 (m-30) REVERT: B 211 ASP cc_start: 0.8750 (t0) cc_final: 0.8505 (t0) REVERT: B 326 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7925 (tptt) REVERT: B 348 SER cc_start: 0.8859 (m) cc_final: 0.8580 (p) REVERT: D 12 MET cc_start: 0.8494 (tmm) cc_final: 0.8101 (ttp) REVERT: D 41 ASP cc_start: 0.8679 (m-30) cc_final: 0.8234 (m-30) REVERT: D 120 ARG cc_start: 0.8573 (ptm-80) cc_final: 0.8192 (ptp90) REVERT: D 135 PHE cc_start: 0.8582 (m-10) cc_final: 0.8376 (m-80) REVERT: D 147 ARG cc_start: 0.7752 (tmm160) cc_final: 0.7495 (ttt-90) REVERT: D 191 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8130 (mm-30) REVERT: D 422 PRO cc_start: 0.4706 (Cg_endo) cc_final: 0.4123 (Cg_exo) REVERT: D 504 MET cc_start: 0.8551 (mmt) cc_final: 0.8348 (mmt) REVERT: D 546 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8070 (mt-10) REVERT: D 641 PHE cc_start: 0.7968 (m-80) cc_final: 0.7657 (m-80) outliers start: 10 outliers final: 7 residues processed: 143 average time/residue: 0.1145 time to fit residues: 25.7183 Evaluate side-chains 137 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 477 TYR Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 34 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 163 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.102847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.076751 restraints weight = 53673.474| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.23 r_work: 0.2728 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14557 Z= 0.137 Angle : 0.560 7.817 19730 Z= 0.275 Chirality : 0.044 0.229 2171 Planarity : 0.004 0.057 2541 Dihedral : 8.700 138.516 1999 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.94 % Favored : 96.95 % Rotamer: Outliers : 0.85 % Allowed : 8.93 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.20), residues: 1774 helix: 1.10 (0.19), residues: 805 sheet: 0.56 (0.30), residues: 283 loop : -0.37 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 430 TYR 0.009 0.001 TYR B 143 PHE 0.010 0.001 PHE D 464 TRP 0.014 0.002 TRP B 79 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00325 (14557) covalent geometry : angle 0.56025 (19730) hydrogen bonds : bond 0.03472 ( 693) hydrogen bonds : angle 4.52985 ( 1884) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: B 25 ASP cc_start: 0.8182 (m-30) cc_final: 0.7925 (m-30) REVERT: B 211 ASP cc_start: 0.8787 (t0) cc_final: 0.8553 (t0) REVERT: B 326 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7953 (tptt) REVERT: B 348 SER cc_start: 0.8883 (m) cc_final: 0.8596 (p) REVERT: C 360 GLN cc_start: 0.8532 (tp40) cc_final: 0.8036 (tp40) REVERT: D 41 ASP cc_start: 0.8674 (m-30) cc_final: 0.8284 (m-30) REVERT: D 120 ARG cc_start: 0.8580 (ptm-80) cc_final: 0.8166 (ptp90) REVERT: D 147 ARG cc_start: 0.7846 (tmm160) cc_final: 0.7609 (ttt-90) REVERT: D 191 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8170 (mm-30) REVERT: D 504 MET cc_start: 0.8539 (mmt) cc_final: 0.8133 (mmt) REVERT: D 546 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8208 (mt-10) REVERT: D 641 PHE cc_start: 0.7928 (m-80) cc_final: 0.7606 (m-80) outliers start: 13 outliers final: 10 residues processed: 136 average time/residue: 0.1184 time to fit residues: 25.0398 Evaluate side-chains 138 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 477 TYR Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 131 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 146 optimal weight: 0.1980 chunk 55 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.103500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.077775 restraints weight = 45161.421| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.97 r_work: 0.2753 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14557 Z= 0.119 Angle : 0.550 8.338 19730 Z= 0.269 Chirality : 0.043 0.222 2171 Planarity : 0.004 0.055 2541 Dihedral : 8.615 138.889 1999 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.99 % Favored : 96.89 % Rotamer: Outliers : 0.78 % Allowed : 9.32 % Favored : 89.90 % 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: 0.71 (0.20), residues: 1774 helix: 1.19 (0.19), residues: 805 sheet: 0.57 (0.30), residues: 283 loop : -0.35 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.008 0.001 TYR B 143 PHE 0.024 0.001 PHE D 135 TRP 0.013 0.001 TRP B 79 HIS 0.006 0.001 HIS D 133 Details of bonding type rmsd covalent geometry : bond 0.00275 (14557) covalent geometry : angle 0.54980 (19730) hydrogen bonds : bond 0.03226 ( 693) hydrogen bonds : angle 4.46543 ( 1884) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: B 25 ASP cc_start: 0.8158 (m-30) cc_final: 0.7907 (m-30) REVERT: B 211 ASP cc_start: 0.8652 (t0) cc_final: 0.8432 (t0) REVERT: B 348 SER cc_start: 0.8867 (m) cc_final: 0.8557 (p) REVERT: D 114 TYR cc_start: 0.7260 (m-80) cc_final: 0.6781 (m-80) REVERT: D 120 ARG cc_start: 0.8543 (ptm-80) cc_final: 0.8147 (ptp90) REVERT: D 147 ARG cc_start: 0.7836 (tmm160) cc_final: 0.7601 (ttt-90) REVERT: D 504 MET cc_start: 0.8527 (mmt) cc_final: 0.8114 (mmt) REVERT: D 546 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8238 (mt-10) REVERT: D 571 ASP cc_start: 0.8393 (t70) cc_final: 0.7927 (t70) outliers start: 12 outliers final: 10 residues processed: 146 average time/residue: 0.1201 time to fit residues: 27.2222 Evaluate side-chains 138 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 477 TYR Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 42 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.100559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.074908 restraints weight = 45709.225| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.97 r_work: 0.2704 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14557 Z= 0.209 Angle : 0.608 7.368 19730 Z= 0.302 Chirality : 0.046 0.241 2171 Planarity : 0.004 0.054 2541 Dihedral : 8.776 135.615 1999 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.50 % Favored : 96.38 % Rotamer: Outliers : 1.17 % Allowed : 9.65 % Favored : 89.18 % 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: 1774 helix: 1.01 (0.19), residues: 803 sheet: 0.49 (0.30), residues: 283 loop : -0.51 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 116 TYR 0.013 0.001 TYR D 216 PHE 0.024 0.002 PHE D 143 TRP 0.015 0.002 TRP B 79 HIS 0.006 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00508 (14557) covalent geometry : angle 0.60769 (19730) hydrogen bonds : bond 0.03987 ( 693) hydrogen bonds : angle 4.57555 ( 1884) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.561 Fit side-chains REVERT: A 82 MET cc_start: 0.8699 (tpt) cc_final: 0.8338 (tpt) REVERT: A 325 MET cc_start: 0.8584 (mmp) cc_final: 0.8041 (mmt) REVERT: B 25 ASP cc_start: 0.8209 (m-30) cc_final: 0.7940 (m-30) REVERT: B 348 SER cc_start: 0.8914 (m) cc_final: 0.8601 (p) REVERT: C 353 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.7676 (mp-120) REVERT: C 360 GLN cc_start: 0.8503 (tp40) cc_final: 0.8234 (tp40) REVERT: D 114 TYR cc_start: 0.7480 (m-80) cc_final: 0.6889 (m-80) REVERT: D 120 ARG cc_start: 0.8517 (ptm-80) cc_final: 0.8129 (ptp90) REVERT: D 145 MET cc_start: 0.8290 (ttp) cc_final: 0.7981 (ttt) REVERT: D 147 ARG cc_start: 0.7861 (tmm160) cc_final: 0.7595 (ttt-90) REVERT: D 191 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7899 (mm-30) REVERT: D 504 MET cc_start: 0.8593 (mmt) cc_final: 0.8214 (mmt) REVERT: D 546 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8347 (mt-10) REVERT: D 571 ASP cc_start: 0.8467 (t70) cc_final: 0.8061 (t70) outliers start: 18 outliers final: 17 residues processed: 139 average time/residue: 0.0980 time to fit residues: 21.3708 Evaluate side-chains 143 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 353 GLN Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 477 TYR Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 71 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 174 optimal weight: 0.4980 chunk 112 optimal weight: 8.9990 chunk 127 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 158 optimal weight: 0.2980 chunk 1 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.076320 restraints weight = 54498.386| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.24 r_work: 0.2720 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 14557 Z= 0.128 Angle : 0.555 7.219 19730 Z= 0.273 Chirality : 0.043 0.205 2171 Planarity : 0.004 0.053 2541 Dihedral : 8.626 136.583 1999 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.99 % Favored : 96.89 % Rotamer: Outliers : 0.91 % Allowed : 9.91 % Favored : 89.18 % 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: 0.59 (0.20), residues: 1774 helix: 1.16 (0.19), residues: 803 sheet: 0.40 (0.29), residues: 290 loop : -0.44 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 72 TYR 0.021 0.001 TYR B 166 PHE 0.023 0.001 PHE D 143 TRP 0.015 0.002 TRP B 79 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00304 (14557) covalent geometry : angle 0.55543 (19730) hydrogen bonds : bond 0.03386 ( 693) hydrogen bonds : angle 4.45688 ( 1884) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.488 Fit side-chains REVERT: A 82 MET cc_start: 0.8731 (tpt) cc_final: 0.8411 (tpt) REVERT: A 227 MET cc_start: 0.8671 (mmp) cc_final: 0.8331 (mmp) REVERT: A 325 MET cc_start: 0.8570 (mmp) cc_final: 0.8021 (mmt) REVERT: B 25 ASP cc_start: 0.8257 (m-30) cc_final: 0.7997 (m-30) REVERT: B 211 ASP cc_start: 0.8691 (t0) cc_final: 0.8459 (t0) REVERT: B 348 SER cc_start: 0.8912 (m) cc_final: 0.8558 (p) REVERT: C 353 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.7702 (mp-120) REVERT: D 114 TYR cc_start: 0.7607 (m-80) cc_final: 0.6940 (m-80) REVERT: D 120 ARG cc_start: 0.8541 (ptm-80) cc_final: 0.8165 (ptp90) REVERT: D 145 MET cc_start: 0.8200 (ttp) cc_final: 0.7883 (ttt) REVERT: D 147 ARG cc_start: 0.7866 (tmm160) cc_final: 0.7513 (ttt-90) REVERT: D 191 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7949 (mm-30) REVERT: D 504 MET cc_start: 0.8555 (mmt) cc_final: 0.8184 (mmt) REVERT: D 546 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8344 (mt-10) REVERT: D 571 ASP cc_start: 0.8418 (t70) cc_final: 0.8002 (t70) outliers start: 14 outliers final: 13 residues processed: 143 average time/residue: 0.1058 time to fit residues: 23.9469 Evaluate side-chains 142 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 353 GLN Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 477 TYR Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 52 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.076584 restraints weight = 48263.267| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.06 r_work: 0.2731 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 14557 Z= 0.137 Angle : 0.562 7.772 19730 Z= 0.276 Chirality : 0.044 0.216 2171 Planarity : 0.004 0.053 2541 Dihedral : 8.553 136.151 1999 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.61 % Rotamer: Outliers : 1.04 % Allowed : 10.10 % Favored : 88.85 % 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: 0.64 (0.20), residues: 1774 helix: 1.19 (0.19), residues: 803 sheet: 0.42 (0.29), residues: 290 loop : -0.38 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.016 0.001 TYR B 166 PHE 0.023 0.001 PHE D 143 TRP 0.013 0.002 TRP B 79 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00328 (14557) covalent geometry : angle 0.56222 (19730) hydrogen bonds : bond 0.03379 ( 693) hydrogen bonds : angle 4.42068 ( 1884) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.589 Fit side-chains REVERT: A 82 MET cc_start: 0.8737 (tpt) cc_final: 0.8419 (tpt) REVERT: A 227 MET cc_start: 0.8695 (mmp) cc_final: 0.8392 (mmp) REVERT: A 325 MET cc_start: 0.8542 (mmp) cc_final: 0.7996 (mmt) REVERT: B 25 ASP cc_start: 0.8233 (m-30) cc_final: 0.7975 (m-30) REVERT: B 211 ASP cc_start: 0.8680 (t0) cc_final: 0.8452 (t0) REVERT: B 348 SER cc_start: 0.8889 (m) cc_final: 0.8576 (p) REVERT: C 353 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.7680 (mp-120) REVERT: C 360 GLN cc_start: 0.8353 (tp40) cc_final: 0.8144 (tp40) REVERT: D 120 ARG cc_start: 0.8517 (ptm-80) cc_final: 0.8140 (ptp90) REVERT: D 145 MET cc_start: 0.8257 (ttp) cc_final: 0.7982 (ttt) REVERT: D 147 ARG cc_start: 0.7875 (tmm160) cc_final: 0.7566 (ttt-90) REVERT: D 504 MET cc_start: 0.8577 (mmt) cc_final: 0.8239 (mmt) REVERT: D 546 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8356 (mt-10) REVERT: D 571 ASP cc_start: 0.8417 (t70) cc_final: 0.7998 (t70) outliers start: 16 outliers final: 14 residues processed: 136 average time/residue: 0.1094 time to fit residues: 23.3955 Evaluate side-chains 139 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 353 GLN Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 477 TYR Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 95 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.100913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.074551 restraints weight = 59395.580| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.37 r_work: 0.2686 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 14557 Z= 0.194 Angle : 0.595 7.844 19730 Z= 0.295 Chirality : 0.045 0.200 2171 Planarity : 0.004 0.053 2541 Dihedral : 8.624 133.360 1999 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.28 % Favored : 96.55 % Rotamer: Outliers : 1.17 % Allowed : 9.97 % Favored : 88.85 % 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: 0.52 (0.20), residues: 1774 helix: 1.07 (0.19), residues: 803 sheet: 0.50 (0.30), residues: 283 loop : -0.50 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.016 0.001 TYR B 166 PHE 0.015 0.001 PHE D 135 TRP 0.014 0.002 TRP B 79 HIS 0.006 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00471 (14557) covalent geometry : angle 0.59521 (19730) hydrogen bonds : bond 0.03810 ( 693) hydrogen bonds : angle 4.49665 ( 1884) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.575 Fit side-chains REVERT: A 82 MET cc_start: 0.8739 (tpt) cc_final: 0.8416 (tpt) REVERT: A 325 MET cc_start: 0.8564 (mmp) cc_final: 0.8023 (mmt) REVERT: B 25 ASP cc_start: 0.8298 (m-30) cc_final: 0.8039 (m-30) REVERT: B 348 SER cc_start: 0.8947 (m) cc_final: 0.8565 (p) REVERT: C 353 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.7700 (mp-120) REVERT: D 120 ARG cc_start: 0.8498 (ptm-80) cc_final: 0.8153 (ptp90) REVERT: D 130 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7823 (mtp) REVERT: D 145 MET cc_start: 0.8339 (ttp) cc_final: 0.8062 (ttt) REVERT: D 147 ARG cc_start: 0.7952 (tmm160) cc_final: 0.7650 (ttt-90) REVERT: D 546 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8416 (mt-10) REVERT: D 571 ASP cc_start: 0.8448 (t70) cc_final: 0.8053 (t70) outliers start: 18 outliers final: 16 residues processed: 135 average time/residue: 0.1107 time to fit residues: 23.4233 Evaluate side-chains 140 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 353 GLN Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 477 TYR Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 170 optimal weight: 0.0370 chunk 31 optimal weight: 0.7980 chunk 133 optimal weight: 10.0000 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.103615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.077428 restraints weight = 53180.405| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.22 r_work: 0.2746 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14557 Z= 0.109 Angle : 0.546 8.104 19730 Z= 0.266 Chirality : 0.043 0.193 2171 Planarity : 0.004 0.054 2541 Dihedral : 8.441 136.771 1999 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.82 % Favored : 97.01 % Rotamer: Outliers : 1.11 % Allowed : 9.97 % Favored : 88.92 % 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: 0.72 (0.21), residues: 1774 helix: 1.26 (0.19), residues: 805 sheet: 0.49 (0.29), residues: 290 loop : -0.37 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.013 0.001 TYR B 166 PHE 0.012 0.001 PHE D 135 TRP 0.013 0.001 TRP B 79 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00253 (14557) covalent geometry : angle 0.54637 (19730) hydrogen bonds : bond 0.03080 ( 693) hydrogen bonds : angle 4.36593 ( 1884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3824.51 seconds wall clock time: 66 minutes 28.50 seconds (3988.50 seconds total)