Starting phenix.real_space_refine on Thu Jul 2 21:53:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pm8_13524/07_2026/7pm8_13524.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pm8_13524/07_2026/7pm8_13524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7pm8_13524/07_2026/7pm8_13524.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pm8_13524/07_2026/7pm8_13524.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pm8_13524/07_2026/7pm8_13524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pm8_13524/07_2026/7pm8_13524.map" model { file = "/net/cci-nas-00/data/ceres_data/7pm8_13524/07_2026/7pm8_13524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pm8_13524/07_2026/7pm8_13524.cif" } resolution = 3.5 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 6462 2.51 5 N 1724 2.21 5 O 1894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10149 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 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} 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: "A" Number of atoms: 6070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 6070 Classifications: {'peptide': 743} Link IDs: {'PTRANS': 27, 'TRANS': 715} Chain breaks: 5 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: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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: 2.01, per 1000 atoms: 0.20 Number of scatterers: 10149 At special positions: 0 Unit cell: (114.48, 142.04, 145.22, 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 1894 8.00 N 1724 7.00 C 6462 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: 0.83 Conformation dependent library (CDL) restraints added in 311.1 milliseconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 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: 2374 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 15 sheets defined 56.0% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 removed outlier: 3.722A pdb=" N VAL A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 70' Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 116 through 119 removed outlier: 3.858A 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 153 removed outlier: 3.763A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 185 removed outlier: 3.891A pdb=" N GLY A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 207 Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.154A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.661A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 316 removed outlier: 3.576A pdb=" N MET A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.644A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 removed outlier: 3.908A pdb=" N THR A 358 " --> pdb=" O HIS A 354 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 removed outlier: 3.500A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 removed outlier: 3.723A pdb=" N ALA A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 480 Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.834A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 499 " --> pdb=" O CYS A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.602A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.648A pdb=" N ALA A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.692A pdb=" N LYS A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 583 removed outlier: 3.820A pdb=" N SER A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 4.073A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 633 Processing helix chain 'A' and resid 635 through 652 Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.706A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 removed outlier: 3.538A pdb=" N GLY A 697 " --> pdb=" O ILE A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 716 through 720 Processing helix chain 'A' and resid 723 through 732 Processing helix chain 'A' and resid 733 through 735 No H-bonds generated for 'chain 'A' and resid 733 through 735' Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.217A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.718A 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 66 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.523A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.551A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.758A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.893A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.711A 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 196 removed outlier: 3.686A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.867A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.633A pdb=" N ARG C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix removed outlier: 3.977A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.664A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 296 removed outlier: 3.763A pdb=" N ARG C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.991A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.593A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 347 removed outlier: 3.507A pdb=" N SER C 338 " --> pdb=" O GLU C 334 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TRP C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 349 No H-bonds generated for 'chain 'C' and resid 348 through 349' Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.544A 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 373 removed outlier: 3.712A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103 removed outlier: 3.698A pdb=" N SER A 162 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 431 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 211 removed outlier: 6.220A pdb=" N ALA A 209 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASN A 216 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.613A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 380 Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA7, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.791A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 27 through 28 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 105 Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.541A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.412A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 515 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: 1.51 Time building geometry restraints manager: 1.14 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: 2742 1.44 - 1.56: 5827 1.56 - 1.68: 6 1.68 - 1.81: 102 Bond restraints: 10364 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 3.72e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.201 0.062 2.00e-02 2.50e+03 9.49e+00 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.370 -0.041 1.40e-02 5.10e+03 8.67e+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 8.59e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.69e+00 ... (remaining 10359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 13648 2.38 - 4.77: 305 4.77 - 7.15: 32 7.15 - 9.53: 10 9.53 - 11.92: 5 Bond angle restraints: 14000 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 121.70 109.78 11.92 1.80e+00 3.09e-01 4.38e+01 angle pdb=" C TYR A 113 " pdb=" N GLU A 114 " pdb=" CA GLU A 114 " ideal model delta sigma weight residual 121.75 129.28 -7.53 1.73e+00 3.34e-01 1.90e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.78 -4.78 1.10e+00 8.26e-01 1.89e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 102.08 8.02 1.90e+00 2.77e-01 1.78e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 118.25 4.15 1.00e+00 1.00e+00 1.72e+01 ... (remaining 13995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.71: 6088 31.71 - 63.42: 115 63.42 - 95.13: 38 95.13 - 126.84: 1 126.84 - 158.56: 2 Dihedral angle restraints: 6244 sinusoidal: 2562 harmonic: 3682 Sorted by residual: 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 98.55 -158.56 1 2.00e+01 2.50e-03 4.63e+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 73.47 -133.47 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 179.67 120.34 1 2.00e+01 2.50e-03 3.61e+01 ... (remaining 6241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.020: 1528 1.020 - 2.040: 0 2.040 - 3.060: 0 3.060 - 4.080: 0 4.080 - 5.100: 2 Chirality restraints: 1530 Sorted by residual: chirality pdb=" CB DTH H 4 " pdb=" CA DTH H 4 " pdb=" OG1 DTH H 4 " pdb=" CG2 DTH H 4 " both_signs ideal model delta sigma weight residual False 2.55 -2.55 5.10 2.00e-01 2.50e+01 6.50e+02 chirality pdb=" CA DTH H 4 " pdb=" N DTH H 4 " pdb=" C DTH H 4 " pdb=" CB DTH H 4 " both_signs ideal model delta sigma weight residual False 2.53 -2.40 4.92 2.00e-01 2.50e+01 6.06e+02 chirality pdb=" CA TYR A 787 " pdb=" N TYR A 787 " pdb=" C TYR A 787 " pdb=" CB TYR A 787 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1527 not shown) Planarity restraints: 1787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 95 " -0.128 9.50e-02 1.11e+02 7.43e-02 2.97e+01 pdb=" NE ARG C 95 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG C 95 " -0.090 2.00e-02 2.50e+03 pdb=" NH1 ARG C 95 " 0.032 2.00e-02 2.50e+03 pdb=" NH2 ARG C 95 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 213 " -0.370 9.50e-02 1.11e+02 1.69e-01 2.80e+01 pdb=" NE ARG A 213 " 0.003 2.00e-02 2.50e+03 pdb=" CZ ARG A 213 " 0.062 2.00e-02 2.50e+03 pdb=" NH1 ARG A 213 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A 213 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 89 " -0.023 2.00e-02 2.50e+03 4.54e-02 2.06e+01 pdb=" C THR C 89 " 0.079 2.00e-02 2.50e+03 pdb=" O THR C 89 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE C 90 " -0.026 2.00e-02 2.50e+03 ... (remaining 1784 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 18 2.37 - 3.00: 5560 3.00 - 3.63: 15137 3.63 - 4.27: 22533 4.27 - 4.90: 38335 Nonbonded interactions: 81583 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 2.074 2.170 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.162 3.040 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.166 2.170 nonbonded pdb=" OG1 THR A 170 " pdb="MG MG A1901 " model vdw 2.171 2.170 ... (remaining 81578 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: 3.350 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.640 Find NCS groups from input model: 0.020 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 : 0.004 0.122 10366 Z= 0.218 Angle : 0.885 11.918 14006 Z= 0.514 Chirality : 0.188 5.100 1530 Planarity : 0.009 0.169 1785 Dihedral : 15.570 158.556 3864 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.81 % 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: -1.60 (0.21), residues: 1231 helix: -1.64 (0.17), residues: 587 sheet: 0.15 (0.39), residues: 144 loop : -0.41 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.091 0.010 ARG C 95 TYR 0.033 0.006 TYR A 113 PHE 0.034 0.002 PHE A 673 TRP 0.029 0.003 TRP C 79 HIS 0.007 0.002 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.22 (10364) covalent geometry : angle 0.88066 / 0.51 (14000) hydrogen bonds : bond 0.15531 / 9.95 ( 513) hydrogen bonds : angle 7.27985 / 4.86 ( 1437) link_TRANS : bond 0.00960 / 0.50 ( 2) link_TRANS : angle 4.25759 / 2.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 735 LEU cc_start: 0.8656 (mt) cc_final: 0.8355 (mp) REVERT: B 29 TYR cc_start: 0.8073 (m-80) cc_final: 0.7713 (m-80) outliers start: 1 outliers final: 1 residues processed: 160 average time/residue: 0.1022 time to fit residues: 22.3411 Evaluate side-chains 90 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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: 125 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 ASN A 156 ASN A 200 ASN A 264 GLN A 395 HIS A 463 GLN A 468 HIS A 755 GLN B 75 GLN B 147 HIS C 161 HIS C 162 ASN C 173 HIS ** C 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.068656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.048643 restraints weight = 41402.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.050372 restraints weight = 20024.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.051517 restraints weight = 12560.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.052238 restraints weight = 9182.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.052656 restraints weight = 7459.243| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 10366 Z= 0.262 Angle : 0.748 9.033 14006 Z= 0.392 Chirality : 0.047 0.222 1530 Planarity : 0.005 0.051 1785 Dihedral : 9.707 175.355 1394 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.93 % Allowed : 7.49 % Favored : 91.58 % 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: 0.34 (0.23), residues: 1231 helix: 0.48 (0.20), residues: 604 sheet: 0.43 (0.40), residues: 143 loop : 0.05 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 152 TYR 0.036 0.002 TYR A 179 PHE 0.029 0.002 PHE B 19 TRP 0.012 0.002 TRP C 79 HIS 0.016 0.002 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.26 (10364) covalent geometry : angle 0.74759 / 0.39 (14000) hydrogen bonds : bond 0.04970 / 3.06 ( 513) hydrogen bonds : angle 5.59075 / 3.78 ( 1437) link_TRANS : bond 0.00023 / 0.01 ( 2) link_TRANS : angle 1.00874 / 0.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8710 (mt) REVERT: A 135 MET cc_start: 0.8359 (mmm) cc_final: 0.8042 (mmm) REVERT: A 371 MET cc_start: 0.8338 (mmm) cc_final: 0.8126 (tpp) REVERT: A 476 GLU cc_start: 0.9064 (tp30) cc_final: 0.8838 (tp30) REVERT: A 790 MET cc_start: 0.0936 (ptt) cc_final: -0.0643 (ttt) REVERT: B 29 TYR cc_start: 0.7921 (m-80) cc_final: 0.7650 (m-10) REVERT: C 123 MET cc_start: 0.9023 (tpp) cc_final: 0.8675 (mmm) REVERT: C 217 CYS cc_start: 0.8340 (m) cc_final: 0.8011 (m) outliers start: 10 outliers final: 3 residues processed: 99 average time/residue: 0.0834 time to fit residues: 12.3597 Evaluate side-chains 73 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain C residue 226 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 26 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 100 optimal weight: 0.3980 chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 31 GLN C 12 ASN C 111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.069804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.049667 restraints weight = 41129.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.051467 restraints weight = 19682.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.052626 restraints weight = 12237.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.053364 restraints weight = 8879.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.053760 restraints weight = 7212.052| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10366 Z= 0.143 Angle : 0.622 12.320 14006 Z= 0.320 Chirality : 0.043 0.208 1530 Planarity : 0.004 0.053 1785 Dihedral : 8.649 164.953 1393 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.39 % Allowed : 8.05 % Favored : 90.56 % 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: 0.92 (0.24), residues: 1231 helix: 1.09 (0.21), residues: 610 sheet: 0.66 (0.40), residues: 145 loop : 0.13 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 64 TYR 0.027 0.001 TYR A 179 PHE 0.018 0.001 PHE A 360 TRP 0.010 0.001 TRP C 340 HIS 0.012 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10364) covalent geometry : angle 0.62237 / 0.32 (14000) hydrogen bonds : bond 0.04092 / 2.52 ( 513) hydrogen bonds : angle 5.10330 / 3.46 ( 1437) link_TRANS : bond 0.00195 / 0.10 ( 2) link_TRANS : angle 0.70999 / 0.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 1 TRP cc_start: 0.8963 (m100) cc_final: 0.8499 (m100) REVERT: A 40 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8701 (mt) REVERT: A 135 MET cc_start: 0.8503 (mmm) cc_final: 0.8005 (mmm) REVERT: A 323 MET cc_start: 0.8278 (mmp) cc_final: 0.7997 (tmm) REVERT: A 476 GLU cc_start: 0.9051 (tp30) cc_final: 0.8772 (tp30) REVERT: A 783 MET cc_start: 0.9033 (mmt) cc_final: 0.8697 (mtm) REVERT: B 26 LYS cc_start: 0.7807 (mtmt) cc_final: 0.7568 (mtpp) REVERT: C 81 ASP cc_start: 0.8588 (m-30) cc_final: 0.7989 (m-30) REVERT: C 123 MET cc_start: 0.8902 (tpp) cc_final: 0.8623 (mmm) REVERT: C 217 CYS cc_start: 0.8365 (m) cc_final: 0.7972 (m) outliers start: 15 outliers final: 3 residues processed: 97 average time/residue: 0.0799 time to fit residues: 11.7336 Evaluate side-chains 75 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 111 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 118 optimal weight: 0.0040 chunk 94 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.069140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.049134 restraints weight = 41052.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.050905 restraints weight = 19828.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.052052 restraints weight = 12396.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.052760 restraints weight = 9041.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.053293 restraints weight = 7335.435| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10366 Z= 0.153 Angle : 0.598 10.260 14006 Z= 0.304 Chirality : 0.042 0.213 1530 Planarity : 0.004 0.050 1785 Dihedral : 7.755 134.290 1393 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.57 % Allowed : 8.60 % Favored : 89.82 % 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: 1.16 (0.24), residues: 1231 helix: 1.35 (0.21), residues: 610 sheet: 0.64 (0.40), residues: 147 loop : 0.19 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 95 TYR 0.022 0.001 TYR A 179 PHE 0.016 0.001 PHE C 255 TRP 0.035 0.002 TRP A 781 HIS 0.009 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (10364) covalent geometry : angle 0.59855 / 0.30 (14000) hydrogen bonds : bond 0.03885 / 2.41 ( 513) hydrogen bonds : angle 4.91879 / 3.34 ( 1437) link_TRANS : bond 0.00106 / 0.06 ( 2) link_TRANS : angle 0.20032 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8667 (mt) REVERT: A 132 MET cc_start: 0.7532 (tmm) cc_final: 0.7255 (tmm) REVERT: A 135 MET cc_start: 0.8546 (mmm) cc_final: 0.8281 (mmm) REVERT: A 371 MET cc_start: 0.8386 (tpp) cc_final: 0.7855 (tpp) REVERT: A 476 GLU cc_start: 0.9071 (tp30) cc_final: 0.8859 (tp30) REVERT: C 81 ASP cc_start: 0.8563 (m-30) cc_final: 0.7997 (m-30) REVERT: C 123 MET cc_start: 0.8836 (tpp) cc_final: 0.8592 (mmm) REVERT: C 217 CYS cc_start: 0.8378 (m) cc_final: 0.7988 (m) outliers start: 17 outliers final: 8 residues processed: 91 average time/residue: 0.0806 time to fit residues: 11.3463 Evaluate side-chains 83 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 781 TRP Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 111 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 21 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 0.0020 chunk 120 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 ASN C 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.068652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.048633 restraints weight = 41453.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.050405 restraints weight = 19910.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.051538 restraints weight = 12380.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.052213 restraints weight = 9026.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.052756 restraints weight = 7353.232| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10366 Z= 0.190 Angle : 0.613 11.249 14006 Z= 0.310 Chirality : 0.042 0.219 1530 Planarity : 0.004 0.046 1785 Dihedral : 7.411 118.664 1393 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.39 % Allowed : 9.90 % Favored : 88.71 % 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: 1.15 (0.24), residues: 1231 helix: 1.37 (0.21), residues: 610 sheet: 0.57 (0.41), residues: 147 loop : 0.17 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 95 TYR 0.019 0.001 TYR A 179 PHE 0.020 0.002 PHE B 12 TRP 0.030 0.002 TRP A 781 HIS 0.008 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (10364) covalent geometry : angle 0.61264 / 0.31 (14000) hydrogen bonds : bond 0.03920 / 2.45 ( 513) hydrogen bonds : angle 4.91796 / 3.35 ( 1437) link_TRANS : bond 0.00207 / 0.11 ( 2) link_TRANS : angle 0.15269 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8958 (mp) REVERT: A 135 MET cc_start: 0.8540 (mmm) cc_final: 0.8245 (mmm) REVERT: A 323 MET cc_start: 0.8248 (mmp) cc_final: 0.7930 (tmm) REVERT: A 371 MET cc_start: 0.8415 (tpp) cc_final: 0.7854 (tpp) REVERT: C 81 ASP cc_start: 0.8571 (m-30) cc_final: 0.7995 (m-30) REVERT: C 123 MET cc_start: 0.8897 (tpp) cc_final: 0.8628 (mmm) REVERT: C 217 CYS cc_start: 0.8437 (m) cc_final: 0.8068 (m) outliers start: 15 outliers final: 10 residues processed: 85 average time/residue: 0.0742 time to fit residues: 9.9541 Evaluate side-chains 84 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 781 TRP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain C residue 107 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 101 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 0.0040 chunk 74 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 252 GLN C 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.069724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.049547 restraints weight = 40918.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.051343 restraints weight = 19461.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.052505 restraints weight = 12103.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.053320 restraints weight = 8823.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.053665 restraints weight = 7082.931| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10366 Z= 0.120 Angle : 0.582 11.733 14006 Z= 0.291 Chirality : 0.041 0.212 1530 Planarity : 0.004 0.051 1785 Dihedral : 6.980 107.777 1393 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.39 % Allowed : 10.27 % Favored : 88.34 % 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: 1.30 (0.24), residues: 1231 helix: 1.44 (0.21), residues: 611 sheet: 0.72 (0.41), residues: 145 loop : 0.29 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 95 TYR 0.018 0.001 TYR A 179 PHE 0.026 0.001 PHE B 19 TRP 0.027 0.002 TRP A 781 HIS 0.008 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (10364) covalent geometry : angle 0.58219 / 0.29 (14000) hydrogen bonds : bond 0.03545 / 2.23 ( 513) hydrogen bonds : angle 4.71330 / 3.19 ( 1437) link_TRANS : bond 0.00106 / 0.06 ( 2) link_TRANS : angle 0.16719 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8937 (mp) REVERT: A 132 MET cc_start: 0.7799 (tmm) cc_final: 0.7583 (tmm) REVERT: A 135 MET cc_start: 0.8519 (mmm) cc_final: 0.8174 (mmm) REVERT: A 323 MET cc_start: 0.8250 (mmp) cc_final: 0.7950 (tmm) REVERT: A 371 MET cc_start: 0.8456 (tpp) cc_final: 0.7856 (tpp) REVERT: A 515 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7541 (mtt) REVERT: C 81 ASP cc_start: 0.8478 (m-30) cc_final: 0.7927 (m-30) REVERT: C 205 GLU cc_start: 0.8330 (pt0) cc_final: 0.7950 (pt0) REVERT: C 217 CYS cc_start: 0.8453 (m) cc_final: 0.8010 (m) outliers start: 15 outliers final: 8 residues processed: 97 average time/residue: 0.0851 time to fit residues: 12.3021 Evaluate side-chains 88 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 781 TRP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain C residue 107 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 114 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 82 optimal weight: 30.0000 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.069010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.048882 restraints weight = 40704.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.050659 restraints weight = 19478.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.051764 restraints weight = 12100.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.052561 restraints weight = 8888.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.052932 restraints weight = 7144.587| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10366 Z= 0.148 Angle : 0.613 11.307 14006 Z= 0.301 Chirality : 0.041 0.219 1530 Planarity : 0.004 0.044 1785 Dihedral : 6.887 105.350 1393 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.67 % Allowed : 11.29 % Favored : 87.05 % 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: 1.32 (0.24), residues: 1231 helix: 1.52 (0.21), residues: 611 sheet: 0.56 (0.41), residues: 151 loop : 0.26 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 155 TYR 0.015 0.001 TYR A 179 PHE 0.018 0.001 PHE A 360 TRP 0.026 0.002 TRP A 781 HIS 0.007 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (10364) covalent geometry : angle 0.61357 / 0.30 (14000) hydrogen bonds : bond 0.03593 / 2.27 ( 513) hydrogen bonds : angle 4.68376 / 3.16 ( 1437) link_TRANS : bond 0.00140 / 0.07 ( 2) link_TRANS : angle 0.11694 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8504 (mmm) cc_final: 0.8123 (mmm) REVERT: A 371 MET cc_start: 0.8476 (tpp) cc_final: 0.7884 (tpp) REVERT: A 467 MET cc_start: 0.8835 (tpp) cc_final: 0.8627 (mmp) REVERT: A 476 GLU cc_start: 0.9107 (tp30) cc_final: 0.8867 (tp30) REVERT: A 515 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7534 (mtt) REVERT: A 648 MET cc_start: 0.8687 (mmm) cc_final: 0.8354 (mmm) REVERT: B 26 LYS cc_start: 0.7671 (mtmt) cc_final: 0.7429 (mtpp) REVERT: C 81 ASP cc_start: 0.8498 (m-30) cc_final: 0.7989 (m-30) REVERT: C 205 GLU cc_start: 0.8443 (pt0) cc_final: 0.7992 (pt0) REVERT: C 217 CYS cc_start: 0.8445 (m) cc_final: 0.8049 (m) outliers start: 18 outliers final: 9 residues processed: 94 average time/residue: 0.0762 time to fit residues: 11.0924 Evaluate side-chains 89 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 781 TRP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 111 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 41 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 ASN A 464 GLN C 111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.068658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.048529 restraints weight = 40761.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.050321 restraints weight = 19492.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.051431 restraints weight = 12117.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.052167 restraints weight = 8875.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.052539 restraints weight = 7206.468| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10366 Z= 0.159 Angle : 0.628 12.740 14006 Z= 0.308 Chirality : 0.042 0.213 1530 Planarity : 0.004 0.047 1785 Dihedral : 6.863 105.962 1393 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.39 % Allowed : 11.84 % Favored : 86.77 % 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: 1.32 (0.25), residues: 1231 helix: 1.54 (0.22), residues: 609 sheet: 0.53 (0.42), residues: 151 loop : 0.25 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 692 TYR 0.010 0.001 TYR A 456 PHE 0.032 0.001 PHE B 12 TRP 0.026 0.002 TRP A 781 HIS 0.007 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (10364) covalent geometry : angle 0.62764 / 0.31 (14000) hydrogen bonds : bond 0.03665 / 2.30 ( 513) hydrogen bonds : angle 4.73044 / 3.19 ( 1437) link_TRANS : bond 0.00153 / 0.08 ( 2) link_TRANS : angle 0.13108 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8496 (mmm) cc_final: 0.8111 (mmm) REVERT: A 323 MET cc_start: 0.8212 (mmp) cc_final: 0.7969 (tmm) REVERT: A 339 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8195 (mm-30) REVERT: A 371 MET cc_start: 0.8471 (tpp) cc_final: 0.7903 (tpp) REVERT: A 476 GLU cc_start: 0.9102 (tp30) cc_final: 0.8862 (tp30) REVERT: A 515 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7500 (mtt) REVERT: A 648 MET cc_start: 0.8712 (mmm) cc_final: 0.8392 (mmm) REVERT: C 81 ASP cc_start: 0.8460 (m-30) cc_final: 0.7951 (m-30) REVERT: C 217 CYS cc_start: 0.8447 (m) cc_final: 0.8071 (m) REVERT: C 325 MET cc_start: 0.8801 (mmt) cc_final: 0.8442 (mmt) outliers start: 15 outliers final: 10 residues processed: 91 average time/residue: 0.0741 time to fit residues: 10.3916 Evaluate side-chains 89 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 781 TRP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 111 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 65 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN A 560 GLN C 111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.069207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.049045 restraints weight = 40733.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.050861 restraints weight = 19426.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.051975 restraints weight = 12020.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.052728 restraints weight = 8791.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.053118 restraints weight = 7120.621| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10366 Z= 0.134 Angle : 0.615 11.751 14006 Z= 0.303 Chirality : 0.041 0.208 1530 Planarity : 0.004 0.046 1785 Dihedral : 6.731 103.055 1393 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.30 % Allowed : 12.30 % Favored : 86.40 % 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: 1.32 (0.25), residues: 1231 helix: 1.59 (0.22), residues: 607 sheet: 0.44 (0.41), residues: 151 loop : 0.22 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 155 TYR 0.010 0.001 TYR A 456 PHE 0.019 0.001 PHE A 360 TRP 0.026 0.002 TRP A 781 HIS 0.006 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (10364) covalent geometry : angle 0.61558 / 0.30 (14000) hydrogen bonds : bond 0.03519 / 2.21 ( 513) hydrogen bonds : angle 4.66571 / 3.14 ( 1437) link_TRANS : bond 0.00115 / 0.06 ( 2) link_TRANS : angle 0.11814 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7544 (tmm) cc_final: 0.7259 (tmm) REVERT: A 135 MET cc_start: 0.8496 (mmm) cc_final: 0.8116 (mmm) REVERT: A 323 MET cc_start: 0.8173 (mmp) cc_final: 0.7904 (tmm) REVERT: A 339 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8203 (mm-30) REVERT: A 371 MET cc_start: 0.8448 (tpp) cc_final: 0.7885 (tpp) REVERT: A 476 GLU cc_start: 0.9097 (tp30) cc_final: 0.8854 (tp30) REVERT: A 515 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7521 (mtt) REVERT: A 648 MET cc_start: 0.8729 (mmm) cc_final: 0.8440 (mmm) REVERT: C 81 ASP cc_start: 0.8393 (m-30) cc_final: 0.7886 (m-30) REVERT: C 132 MET cc_start: 0.9045 (tmm) cc_final: 0.8761 (tmm) REVERT: C 217 CYS cc_start: 0.8415 (m) cc_final: 0.8025 (m) REVERT: C 325 MET cc_start: 0.8810 (mmt) cc_final: 0.8452 (mmt) outliers start: 14 outliers final: 9 residues processed: 91 average time/residue: 0.0788 time to fit residues: 11.1703 Evaluate side-chains 89 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 781 TRP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 111 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 0.0270 chunk 86 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 252 GLN A 464 GLN C 111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.068046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.048029 restraints weight = 40323.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.049761 restraints weight = 19463.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.050868 restraints weight = 12155.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.051452 restraints weight = 8899.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.052011 restraints weight = 7415.151| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10366 Z= 0.196 Angle : 0.657 15.476 14006 Z= 0.323 Chirality : 0.042 0.216 1530 Planarity : 0.004 0.047 1785 Dihedral : 6.847 106.353 1393 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.11 % Allowed : 12.58 % Favored : 86.31 % 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: 1.23 (0.25), residues: 1231 helix: 1.52 (0.21), residues: 608 sheet: 0.37 (0.42), residues: 151 loop : 0.17 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 155 TYR 0.010 0.001 TYR A 456 PHE 0.023 0.002 PHE A 360 TRP 0.026 0.002 TRP A 781 HIS 0.006 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (10364) covalent geometry : angle 0.65724 / 0.32 (14000) hydrogen bonds : bond 0.03777 / 2.38 ( 513) hydrogen bonds : angle 4.78919 / 3.23 ( 1437) link_TRANS : bond 0.00185 / 0.10 ( 2) link_TRANS : angle 0.13510 / 0.08 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7481 (tmm) cc_final: 0.7226 (tmm) REVERT: A 135 MET cc_start: 0.8478 (mmm) cc_final: 0.8092 (mmm) REVERT: A 323 MET cc_start: 0.8248 (mmp) cc_final: 0.7967 (tmm) REVERT: A 339 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8205 (mm-30) REVERT: A 371 MET cc_start: 0.8451 (tpp) cc_final: 0.7902 (tpp) REVERT: A 515 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7536 (mtt) REVERT: A 648 MET cc_start: 0.8711 (mmm) cc_final: 0.8409 (mmm) REVERT: B 65 VAL cc_start: 0.6400 (OUTLIER) cc_final: 0.6072 (p) REVERT: C 81 ASP cc_start: 0.8346 (m-30) cc_final: 0.7862 (m-30) REVERT: C 132 MET cc_start: 0.9095 (tmm) cc_final: 0.8827 (tmm) REVERT: C 217 CYS cc_start: 0.8507 (m) cc_final: 0.8219 (m) REVERT: C 325 MET cc_start: 0.8791 (mmt) cc_final: 0.8436 (mmt) outliers start: 12 outliers final: 10 residues processed: 89 average time/residue: 0.0747 time to fit residues: 10.3894 Evaluate side-chains 89 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 781 TRP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 111 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 44 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 HIS A 406 HIS A 576 GLN B 31 GLN C 111 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.066458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.046284 restraints weight = 41544.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.047989 restraints weight = 20282.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.049085 restraints weight = 12742.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.049758 restraints weight = 9408.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.050249 restraints weight = 7734.308| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 10366 Z= 0.312 Angle : 0.733 11.607 14006 Z= 0.369 Chirality : 0.045 0.235 1530 Planarity : 0.004 0.046 1785 Dihedral : 7.228 109.981 1393 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.39 % Allowed : 12.30 % Favored : 86.31 % 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: 0.90 (0.24), residues: 1231 helix: 1.28 (0.21), residues: 601 sheet: 0.19 (0.42), residues: 151 loop : -0.02 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 64 TYR 0.017 0.002 TYR A 263 PHE 0.023 0.002 PHE B 12 TRP 0.025 0.002 TRP A 781 HIS 0.008 0.001 HIS C 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00696 / 0.31 (10364) covalent geometry : angle 0.73316 / 0.37 (14000) hydrogen bonds : bond 0.04311 / 2.72 ( 513) hydrogen bonds : angle 5.10553 / 3.47 ( 1437) link_TRANS : bond 0.00300 / 0.16 ( 2) link_TRANS : angle 0.27752 / 0.17 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1818.29 seconds wall clock time: 32 minutes 19.75 seconds (1939.75 seconds total)