Starting phenix.real_space_refine on Wed Mar 4 03:22:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pmb_13527/03_2026/7pmb_13527.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pmb_13527/03_2026/7pmb_13527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pmb_13527/03_2026/7pmb_13527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pmb_13527/03_2026/7pmb_13527.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pmb_13527/03_2026/7pmb_13527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pmb_13527/03_2026/7pmb_13527.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 4 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 6441 2.51 5 N 1719 2.21 5 O 1884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10113 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 739, 6043 Classifications: {'peptide': 739} Link IDs: {'PTRANS': 27, 'TRANS': 711} Chain breaks: 6 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" 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 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: "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} Time building chain proxies: 1.81, per 1000 atoms: 0.18 Number of scatterers: 10113 At special positions: 0 Unit cell: (107.06, 136.74, 150.52, 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 63 16.00 P 4 15.00 Mg 2 11.99 O 1884 8.00 N 1719 7.00 C 6441 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 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 423.6 milliseconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 14 sheets defined 56.0% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.175A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.769A pdb=" N LEU A 77 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 95 removed outlier: 3.543A pdb=" N ARG A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.184A pdb=" N TYR A 119 " --> pdb=" O LEU A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 154 removed outlier: 3.720A pdb=" N ALA A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 185 Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.954A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 251 removed outlier: 4.148A pdb=" N VAL A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.191A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.535A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.886A pdb=" N MET A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 338 removed outlier: 3.590A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 removed outlier: 3.700A pdb=" N PHE A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 removed outlier: 3.965A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 removed outlier: 3.590A pdb=" N ILE A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.831A pdb=" N LEU A 486 " --> pdb=" O PRO A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.522A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.591A pdb=" N CYS A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.625A pdb=" N GLN A 525 " --> pdb=" O ASP A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.627A pdb=" N LYS A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.643A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.920A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 removed outlier: 4.038A pdb=" N LYS A 634 " --> pdb=" O LYS A 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 630 through 634' Processing helix chain 'A' and resid 635 through 652 Processing helix chain 'A' and resid 674 through 685 removed outlier: 4.056A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 704 through 713 removed outlier: 4.438A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 736 removed outlier: 4.145A pdb=" N ASN A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 792 removed outlier: 3.580A pdb=" N TRP A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.675A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.925A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.860A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.885A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.846A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.783A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.880A pdb=" N ARG C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 257' Processing helix chain 'C' and resid 258 through 263 removed outlier: 4.118A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 286 through 296 removed outlier: 4.496A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.989A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.522A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) 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 349 removed outlier: 3.611A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.974A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.722A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 3.561A pdb=" N LEU A 107 " --> pdb=" O TYR A 658 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER A 158 " --> pdb=" O HIS A 657 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER A 431 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 382 Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA8, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.888A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.980A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.464A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 241 512 hydrogen bonds defined for protein. 1437 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: 1.38 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1687 1.32 - 1.44: 2731 1.44 - 1.57: 5801 1.57 - 1.69: 6 1.69 - 1.81: 102 Bond restraints: 10327 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.450 0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.202 0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.463 0.062 2.10e-02 2.27e+03 8.60e+00 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.369 -0.040 1.40e-02 5.10e+03 8.33e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.33e+00 ... (remaining 10322 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 13543 2.38 - 4.76: 349 4.76 - 7.14: 45 7.14 - 9.51: 7 9.51 - 11.89: 4 Bond angle restraints: 13948 Sorted by residual: angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 109.81 11.89 1.80e+00 3.09e-01 4.37e+01 angle pdb=" CA TRP C 356 " pdb=" CB TRP C 356 " pdb=" CG TRP C 356 " ideal model delta sigma weight residual 113.60 122.80 -9.20 1.90e+00 2.77e-01 2.34e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.81 -4.81 1.10e+00 8.26e-01 1.91e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 102.06 8.04 1.90e+00 2.77e-01 1.79e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 118.21 4.19 1.00e+00 1.00e+00 1.75e+01 ... (remaining 13943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.17: 5978 27.17 - 54.34: 198 54.34 - 81.51: 41 81.51 - 108.69: 9 108.69 - 135.86: 4 Dihedral angle restraints: 6230 sinusoidal: 2564 harmonic: 3666 Sorted by residual: 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 75.86 -135.86 1 2.00e+01 2.50e-03 4.12e+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 71.60 -131.60 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" O1B ADP A1902 " pdb=" O3A ADP A1902 " pdb=" PB ADP A1902 " pdb=" PA ADP A1902 " ideal model delta sinusoidal sigma weight residual -60.00 67.63 -127.64 1 2.00e+01 2.50e-03 3.87e+01 ... (remaining 6227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1165 0.059 - 0.118: 287 0.118 - 0.177: 61 0.177 - 0.236: 9 0.236 - 0.295: 2 Chirality restraints: 1524 Sorted by residual: chirality pdb=" CA TYR A 711 " pdb=" N TYR A 711 " pdb=" C TYR A 711 " pdb=" CB TYR A 711 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA HIS A 418 " pdb=" N HIS A 418 " pdb=" C HIS A 418 " pdb=" CB HIS A 418 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ARG A 213 " pdb=" N ARG A 213 " pdb=" C ARG A 213 " pdb=" CB ARG A 213 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1521 not shown) Planarity restraints: 1779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 28 " 0.133 9.50e-02 1.11e+02 7.79e-02 3.35e+01 pdb=" NE ARG C 28 " -0.041 2.00e-02 2.50e+03 pdb=" CZ ARG C 28 " 0.095 2.00e-02 2.50e+03 pdb=" NH1 ARG C 28 " -0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG C 28 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 677 " 0.140 9.50e-02 1.11e+02 7.83e-02 3.01e+01 pdb=" NE ARG A 677 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG A 677 " 0.090 2.00e-02 2.50e+03 pdb=" NH1 ARG A 677 " -0.032 2.00e-02 2.50e+03 pdb=" NH2 ARG A 677 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 477 " -0.001 2.00e-02 2.50e+03 3.42e-02 2.34e+01 pdb=" CG TYR A 477 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR A 477 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 477 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR A 477 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 477 " -0.049 2.00e-02 2.50e+03 pdb=" CZ TYR A 477 " -0.049 2.00e-02 2.50e+03 pdb=" OH TYR A 477 " 0.050 2.00e-02 2.50e+03 ... (remaining 1776 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 18 2.37 - 3.00: 5558 3.00 - 3.63: 14983 3.63 - 4.27: 22360 4.27 - 4.90: 37639 Nonbonded interactions: 80558 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.732 3.620 nonbonded pdb="MG MG A1901 " pdb=" O1B ADP A1902 " model vdw 1.947 2.170 nonbonded pdb=" OG1 THR A 170 " pdb="MG MG A1901 " model vdw 2.021 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.136 2.170 nonbonded pdb=" OH TYR A 528 " pdb=" O ALA A 547 " model vdw 2.162 3.040 ... (remaining 80553 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.480 Find NCS groups from input model: 0.040 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 10329 Z= 0.279 Angle : 0.936 11.894 13954 Z= 0.545 Chirality : 0.056 0.295 1524 Planarity : 0.009 0.117 1777 Dihedral : 15.861 135.857 3860 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.19 % Favored : 99.72 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.21), residues: 1224 helix: -1.69 (0.17), residues: 566 sheet: 0.17 (0.36), residues: 155 loop : 0.23 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.097 0.013 ARG C 28 TYR 0.050 0.007 TYR A 477 PHE 0.031 0.003 PHE C 255 TRP 0.054 0.004 TRP C 356 HIS 0.008 0.002 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00605 (10327) covalent geometry : angle 0.93188 (13948) hydrogen bonds : bond 0.15763 ( 510) hydrogen bonds : angle 7.48772 ( 1437) link_TRANS : bond 0.00923 ( 2) link_TRANS : angle 4.22853 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.8082 (p0) cc_final: 0.7874 (p0) REVERT: A 790 MET cc_start: -0.0217 (ppp) cc_final: -0.0449 (ptm) REVERT: C 313 MET cc_start: 0.8525 (mmm) cc_final: 0.8321 (tpt) outliers start: 1 outliers final: 1 residues processed: 141 average time/residue: 0.1127 time to fit residues: 21.6915 Evaluate side-chains 80 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0270 chunk 113 optimal weight: 0.0020 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 123 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.4246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 147 HIS A 264 GLN A 290 GLN A 354 HIS A 373 HIS A 395 HIS A 398 ASN A 463 GLN A 755 GLN A 775 GLN C 121 GLN C 161 HIS C 162 ASN C 371 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.073203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.052891 restraints weight = 39503.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.054800 restraints weight = 18910.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.056038 restraints weight = 11691.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.056885 restraints weight = 8433.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.057417 restraints weight = 6702.887| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10329 Z= 0.138 Angle : 0.678 10.301 13954 Z= 0.348 Chirality : 0.044 0.300 1524 Planarity : 0.004 0.045 1777 Dihedral : 10.257 133.236 1398 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 1.39 % Allowed : 5.39 % Favored : 93.22 % 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: 0.92 (0.23), residues: 1224 helix: 0.79 (0.21), residues: 587 sheet: 0.83 (0.38), residues: 150 loop : 0.55 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 152 TYR 0.014 0.001 TYR A 50 PHE 0.028 0.002 PHE C 375 TRP 0.027 0.002 TRP A 484 HIS 0.004 0.001 HIS A 430 Details of bonding type rmsd covalent geometry : bond 0.00300 (10327) covalent geometry : angle 0.67737 (13948) hydrogen bonds : bond 0.04162 ( 510) hydrogen bonds : angle 5.34347 ( 1437) link_TRANS : bond 0.00141 ( 2) link_TRANS : angle 1.12042 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 PHE cc_start: 0.6974 (m-10) cc_final: 0.6601 (m-80) REVERT: B 66 ASP cc_start: 0.7593 (p0) cc_final: 0.7392 (p0) REVERT: A 132 MET cc_start: 0.7399 (ppp) cc_final: 0.6239 (ppp) REVERT: A 788 MET cc_start: 0.5011 (ptp) cc_final: 0.4473 (mtt) REVERT: C 41 GLN cc_start: 0.8446 (tp-100) cc_final: 0.8205 (tm-30) REVERT: C 107 GLU cc_start: 0.7116 (tt0) cc_final: 0.6631 (tt0) REVERT: C 217 CYS cc_start: 0.8721 (m) cc_final: 0.8254 (m) REVERT: C 227 MET cc_start: 0.8629 (tpp) cc_final: 0.8322 (tpp) REVERT: C 313 MET cc_start: 0.8944 (mmm) cc_final: 0.8680 (tpt) outliers start: 15 outliers final: 7 residues processed: 118 average time/residue: 0.0922 time to fit residues: 15.7882 Evaluate side-chains 86 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain C residue 257 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 118 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 105 optimal weight: 0.0370 chunk 117 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 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 = 0.3486 r_free = 0.3486 target = 0.071848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.051659 restraints weight = 39151.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.053556 restraints weight = 18762.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.054798 restraints weight = 11610.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.055624 restraints weight = 8341.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.056041 restraints weight = 6628.175| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10329 Z= 0.155 Angle : 0.614 8.042 13954 Z= 0.312 Chirality : 0.043 0.190 1524 Planarity : 0.004 0.049 1777 Dihedral : 9.025 133.778 1397 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.02 % Allowed : 7.99 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.24), residues: 1224 helix: 1.31 (0.22), residues: 596 sheet: 0.91 (0.40), residues: 144 loop : 0.60 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 343 TYR 0.014 0.001 TYR A 259 PHE 0.014 0.002 PHE C 255 TRP 0.014 0.002 TRP A 414 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00349 (10327) covalent geometry : angle 0.61368 (13948) hydrogen bonds : bond 0.03772 ( 510) hydrogen bonds : angle 5.02478 ( 1437) link_TRANS : bond 0.00235 ( 2) link_TRANS : angle 1.12419 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.5608 (m-80) cc_final: 0.5109 (m-80) REVERT: B 67 PHE cc_start: 0.4003 (t80) cc_final: 0.3316 (t80) REVERT: A 132 MET cc_start: 0.7447 (ppp) cc_final: 0.5916 (ppp) REVERT: A 788 MET cc_start: 0.4661 (ptp) cc_final: 0.4247 (mtt) REVERT: C 217 CYS cc_start: 0.8912 (m) cc_final: 0.8504 (m) REVERT: C 227 MET cc_start: 0.8597 (tpp) cc_final: 0.8246 (tpp) REVERT: C 241 GLU cc_start: 0.8095 (mp0) cc_final: 0.7872 (pm20) outliers start: 11 outliers final: 6 residues processed: 90 average time/residue: 0.0814 time to fit residues: 11.2651 Evaluate side-chains 78 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 777 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 19 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN C 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.070069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.050013 restraints weight = 39384.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.051868 restraints weight = 19026.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.053079 restraints weight = 11766.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.053834 restraints weight = 8467.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.054404 restraints weight = 6802.107| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10329 Z= 0.226 Angle : 0.654 9.200 13954 Z= 0.329 Chirality : 0.044 0.182 1524 Planarity : 0.004 0.041 1777 Dihedral : 8.619 137.003 1397 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.86 % Allowed : 10.12 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.24), residues: 1224 helix: 1.24 (0.22), residues: 606 sheet: 0.96 (0.41), residues: 139 loop : 0.42 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 64 TYR 0.014 0.002 TYR A 259 PHE 0.021 0.002 PHE B 12 TRP 0.014 0.002 TRP C 79 HIS 0.005 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00506 (10327) covalent geometry : angle 0.65420 (13948) hydrogen bonds : bond 0.03954 ( 510) hydrogen bonds : angle 5.03852 ( 1437) link_TRANS : bond 0.00263 ( 2) link_TRANS : angle 1.03720 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 PHE cc_start: 0.7965 (t80) cc_final: 0.7592 (t80) REVERT: B 140 ASN cc_start: 0.9499 (m-40) cc_final: 0.8959 (p0) REVERT: A 132 MET cc_start: 0.7661 (ppp) cc_final: 0.7003 (ppp) REVERT: A 788 MET cc_start: 0.4633 (ptp) cc_final: 0.4161 (mtt) REVERT: C 217 CYS cc_start: 0.8932 (m) cc_final: 0.8623 (m) REVERT: C 227 MET cc_start: 0.8643 (tpp) cc_final: 0.8325 (tpp) outliers start: 20 outliers final: 11 residues processed: 87 average time/residue: 0.0813 time to fit residues: 10.7796 Evaluate side-chains 77 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 149 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 28 optimal weight: 1.9990 chunk 96 optimal weight: 0.0970 chunk 10 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.070503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.050339 restraints weight = 39404.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.052215 restraints weight = 18919.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.053418 restraints weight = 11703.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.054244 restraints weight = 8454.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.054738 restraints weight = 6743.704| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10329 Z= 0.170 Angle : 0.604 8.843 13954 Z= 0.300 Chirality : 0.042 0.180 1524 Planarity : 0.004 0.040 1777 Dihedral : 8.351 135.967 1397 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.67 % Allowed : 10.68 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.24), residues: 1224 helix: 1.39 (0.22), residues: 607 sheet: 0.99 (0.42), residues: 139 loop : 0.30 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 64 TYR 0.014 0.001 TYR A 259 PHE 0.022 0.001 PHE B 19 TRP 0.013 0.002 TRP C 79 HIS 0.015 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00383 (10327) covalent geometry : angle 0.60374 (13948) hydrogen bonds : bond 0.03621 ( 510) hydrogen bonds : angle 4.89046 ( 1437) link_TRANS : bond 0.00228 ( 2) link_TRANS : angle 0.98474 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.5819 (m-80) cc_final: 0.5393 (m-80) REVERT: B 140 ASN cc_start: 0.9528 (m-40) cc_final: 0.9006 (p0) REVERT: A 132 MET cc_start: 0.7700 (ppp) cc_final: 0.7140 (ppp) REVERT: A 788 MET cc_start: 0.4645 (ptp) cc_final: 0.4181 (mtt) REVERT: C 54 VAL cc_start: 0.9266 (t) cc_final: 0.8555 (m) REVERT: C 217 CYS cc_start: 0.8936 (m) cc_final: 0.8608 (m) REVERT: C 227 MET cc_start: 0.8681 (tpp) cc_final: 0.8369 (tpt) outliers start: 18 outliers final: 13 residues processed: 90 average time/residue: 0.0770 time to fit residues: 10.6315 Evaluate side-chains 81 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 777 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 0.0270 chunk 119 optimal weight: 0.3980 chunk 100 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 72 optimal weight: 0.0070 chunk 16 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 GLN C 40 HIS C 111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.072176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.052071 restraints weight = 39022.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.054017 restraints weight = 18547.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.055256 restraints weight = 11370.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.056121 restraints weight = 8154.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.056601 restraints weight = 6444.363| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10329 Z= 0.103 Angle : 0.576 9.558 13954 Z= 0.280 Chirality : 0.041 0.177 1524 Planarity : 0.003 0.038 1777 Dihedral : 7.900 130.603 1397 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.49 % Allowed : 11.61 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.24), residues: 1224 helix: 1.60 (0.22), residues: 607 sheet: 1.24 (0.40), residues: 154 loop : 0.29 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 64 TYR 0.009 0.001 TYR A 456 PHE 0.019 0.001 PHE B 19 TRP 0.016 0.001 TRP A 484 HIS 0.006 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00227 (10327) covalent geometry : angle 0.57551 (13948) hydrogen bonds : bond 0.03172 ( 510) hydrogen bonds : angle 4.67774 ( 1437) link_TRANS : bond 0.00189 ( 2) link_TRANS : angle 0.91946 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.5819 (m-80) cc_final: 0.5315 (m-80) REVERT: B 68 GLU cc_start: 0.9353 (mp0) cc_final: 0.9051 (pm20) REVERT: B 119 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.8762 (mmtm) REVERT: A 132 MET cc_start: 0.7590 (ppp) cc_final: 0.7160 (ppp) REVERT: A 788 MET cc_start: 0.4589 (ptp) cc_final: 0.4123 (mtt) REVERT: C 217 CYS cc_start: 0.8926 (m) cc_final: 0.8573 (m) REVERT: C 227 MET cc_start: 0.8621 (tpp) cc_final: 0.8317 (tpt) outliers start: 16 outliers final: 11 residues processed: 89 average time/residue: 0.0955 time to fit residues: 12.5250 Evaluate side-chains 82 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 111 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 41 optimal weight: 0.0170 chunk 6 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN C 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.071925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.051920 restraints weight = 38630.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.053838 restraints weight = 18462.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.055083 restraints weight = 11342.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.055845 restraints weight = 8116.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.056430 restraints weight = 6523.668| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10329 Z= 0.113 Angle : 0.589 9.829 13954 Z= 0.284 Chirality : 0.040 0.178 1524 Planarity : 0.004 0.057 1777 Dihedral : 7.699 125.075 1397 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.58 % Allowed : 12.35 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.24), residues: 1224 helix: 1.64 (0.22), residues: 607 sheet: 1.25 (0.40), residues: 154 loop : 0.24 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 343 TYR 0.010 0.001 TYR A 259 PHE 0.019 0.001 PHE B 19 TRP 0.018 0.001 TRP A 484 HIS 0.005 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00255 (10327) covalent geometry : angle 0.58870 (13948) hydrogen bonds : bond 0.03176 ( 510) hydrogen bonds : angle 4.61522 ( 1437) link_TRANS : bond 0.00201 ( 2) link_TRANS : angle 0.88301 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.5811 (m-80) cc_final: 0.5576 (m-80) REVERT: B 68 GLU cc_start: 0.9519 (mp0) cc_final: 0.9247 (mp0) REVERT: A 788 MET cc_start: 0.4372 (ptp) cc_final: 0.3912 (mtt) REVERT: C 217 CYS cc_start: 0.8916 (m) cc_final: 0.8566 (m) REVERT: C 227 MET cc_start: 0.8572 (tpp) cc_final: 0.8297 (tpt) REVERT: C 313 MET cc_start: 0.9082 (tpt) cc_final: 0.8522 (mmt) outliers start: 17 outliers final: 11 residues processed: 87 average time/residue: 0.0852 time to fit residues: 11.1925 Evaluate side-chains 82 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 153 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 66 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.071453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.051402 restraints weight = 38814.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.053292 restraints weight = 18659.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.054520 restraints weight = 11471.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.055317 restraints weight = 8233.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.055810 restraints weight = 6590.253| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10329 Z= 0.130 Angle : 0.601 10.658 13954 Z= 0.287 Chirality : 0.040 0.177 1524 Planarity : 0.003 0.046 1777 Dihedral : 7.557 121.602 1397 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.11 % Allowed : 13.56 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.24), residues: 1224 helix: 1.66 (0.22), residues: 607 sheet: 1.23 (0.40), residues: 154 loop : 0.23 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 343 TYR 0.012 0.001 TYR A 259 PHE 0.016 0.001 PHE B 19 TRP 0.015 0.001 TRP A 484 HIS 0.004 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00296 (10327) covalent geometry : angle 0.60074 (13948) hydrogen bonds : bond 0.03204 ( 510) hydrogen bonds : angle 4.59019 ( 1437) link_TRANS : bond 0.00217 ( 2) link_TRANS : angle 0.87735 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.5918 (m-80) cc_final: 0.5610 (m-80) REVERT: B 68 GLU cc_start: 0.9536 (mp0) cc_final: 0.9268 (mp0) REVERT: A 132 MET cc_start: 0.7412 (ppp) cc_final: 0.6637 (ppp) REVERT: A 788 MET cc_start: 0.4236 (ptp) cc_final: 0.3801 (mtt) REVERT: C 217 CYS cc_start: 0.8937 (m) cc_final: 0.8587 (m) REVERT: C 227 MET cc_start: 0.8554 (tpp) cc_final: 0.8280 (tpt) outliers start: 12 outliers final: 11 residues processed: 84 average time/residue: 0.0847 time to fit residues: 10.9010 Evaluate side-chains 83 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 153 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 97 optimal weight: 0.0670 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.071375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.051167 restraints weight = 39189.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.053064 restraints weight = 18871.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.054290 restraints weight = 11661.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.055097 restraints weight = 8410.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.055623 restraints weight = 6711.855| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10329 Z= 0.129 Angle : 0.613 11.013 13954 Z= 0.291 Chirality : 0.040 0.175 1524 Planarity : 0.003 0.042 1777 Dihedral : 7.464 119.702 1397 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.21 % Allowed : 13.56 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.24), residues: 1224 helix: 1.70 (0.22), residues: 604 sheet: 1.24 (0.41), residues: 154 loop : 0.25 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 343 TYR 0.012 0.001 TYR A 259 PHE 0.017 0.001 PHE B 19 TRP 0.020 0.002 TRP A 484 HIS 0.004 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00294 (10327) covalent geometry : angle 0.61312 (13948) hydrogen bonds : bond 0.03176 ( 510) hydrogen bonds : angle 4.61738 ( 1437) link_TRANS : bond 0.00213 ( 2) link_TRANS : angle 0.85928 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.5932 (m-80) cc_final: 0.5368 (m-80) REVERT: B 68 GLU cc_start: 0.9444 (mp0) cc_final: 0.9164 (mp0) REVERT: A 132 MET cc_start: 0.7321 (ppp) cc_final: 0.6542 (ppp) REVERT: A 500 GLU cc_start: 0.8319 (tt0) cc_final: 0.7907 (tm-30) REVERT: A 788 MET cc_start: 0.4243 (ptp) cc_final: 0.3757 (mtt) REVERT: C 217 CYS cc_start: 0.8935 (m) cc_final: 0.8590 (m) REVERT: C 227 MET cc_start: 0.8559 (tpp) cc_final: 0.8288 (tpt) outliers start: 13 outliers final: 12 residues processed: 85 average time/residue: 0.0855 time to fit residues: 11.0286 Evaluate side-chains 84 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 153 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 75 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 55 optimal weight: 0.0030 chunk 12 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.071730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.051659 restraints weight = 38043.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.053559 restraints weight = 18341.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.054763 restraints weight = 11352.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.055568 restraints weight = 8196.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.056064 restraints weight = 6558.690| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10329 Z= 0.119 Angle : 0.620 11.467 13954 Z= 0.292 Chirality : 0.040 0.175 1524 Planarity : 0.003 0.040 1777 Dihedral : 7.338 117.474 1397 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.21 % Allowed : 13.56 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.24), residues: 1224 helix: 1.69 (0.22), residues: 604 sheet: 1.27 (0.41), residues: 154 loop : 0.26 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 343 TYR 0.014 0.001 TYR A 787 PHE 0.026 0.001 PHE B 67 TRP 0.020 0.001 TRP A 484 HIS 0.004 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00273 (10327) covalent geometry : angle 0.62029 (13948) hydrogen bonds : bond 0.03119 ( 510) hydrogen bonds : angle 4.58716 ( 1437) link_TRANS : bond 0.00212 ( 2) link_TRANS : angle 0.86573 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.5704 (m-80) cc_final: 0.5394 (m-80) REVERT: B 68 GLU cc_start: 0.9476 (mp0) cc_final: 0.9189 (mp0) REVERT: B 119 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8870 (mmtt) REVERT: A 132 MET cc_start: 0.7314 (ppp) cc_final: 0.6546 (ppp) REVERT: A 500 GLU cc_start: 0.8341 (tt0) cc_final: 0.7914 (tm-30) REVERT: A 788 MET cc_start: 0.4388 (ptp) cc_final: 0.3906 (mtt) REVERT: C 217 CYS cc_start: 0.8916 (m) cc_final: 0.8572 (m) REVERT: C 227 MET cc_start: 0.8523 (tpp) cc_final: 0.8315 (tpp) outliers start: 13 outliers final: 12 residues processed: 84 average time/residue: 0.0876 time to fit residues: 11.0374 Evaluate side-chains 85 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 153 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 116 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.071531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.051400 restraints weight = 38542.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.053307 restraints weight = 18513.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.054553 restraints weight = 11451.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.055356 restraints weight = 8208.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.055904 restraints weight = 6540.827| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10329 Z= 0.128 Angle : 0.626 11.073 13954 Z= 0.295 Chirality : 0.041 0.174 1524 Planarity : 0.003 0.039 1777 Dihedral : 7.289 116.935 1397 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.11 % Allowed : 13.74 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.24), residues: 1224 helix: 1.69 (0.22), residues: 604 sheet: 1.30 (0.41), residues: 154 loop : 0.28 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 343 TYR 0.011 0.001 TYR A 259 PHE 0.022 0.001 PHE B 67 TRP 0.019 0.001 TRP A 484 HIS 0.004 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00293 (10327) covalent geometry : angle 0.62596 (13948) hydrogen bonds : bond 0.03167 ( 510) hydrogen bonds : angle 4.60155 ( 1437) link_TRANS : bond 0.00223 ( 2) link_TRANS : angle 0.86361 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1961.15 seconds wall clock time: 34 minutes 25.07 seconds (2065.07 seconds total)