Starting phenix.real_space_refine on Mon Jul 28 14:54:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pmb_13527/07_2025/7pmb_13527.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pmb_13527/07_2025/7pmb_13527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pmb_13527/07_2025/7pmb_13527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pmb_13527/07_2025/7pmb_13527.map" model { file = "/net/cci-nas-00/data/ceres_data/7pmb_13527/07_2025/7pmb_13527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pmb_13527/07_2025/7pmb_13527.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 6441 2.51 5 N 1719 2.21 5 O 1884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10113 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 739, 6043 Classifications: {'peptide': 739} Link IDs: {'PTRANS': 27, 'TRANS': 711} Chain breaks: 6 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.07, per 1000 atoms: 0.70 Number of scatterers: 10113 At special positions: 0 Unit cell: (107.06, 136.74, 150.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 4 15.00 Mg 2 11.99 O 1884 8.00 N 1719 7.00 C 6441 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.4 seconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 14 sheets defined 56.0% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.175A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.769A pdb=" N LEU A 77 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 95 removed outlier: 3.543A pdb=" N ARG A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.184A pdb=" N TYR A 119 " --> pdb=" O LEU A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 154 removed outlier: 3.720A pdb=" N ALA A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 185 Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.954A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 251 removed outlier: 4.148A pdb=" N VAL A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.191A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.535A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.886A pdb=" N MET A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 338 removed outlier: 3.590A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 removed outlier: 3.700A pdb=" N PHE A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 removed outlier: 3.965A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 removed outlier: 3.590A pdb=" N ILE A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.831A pdb=" N LEU A 486 " --> pdb=" O PRO A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.522A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.591A pdb=" N CYS A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.625A pdb=" N GLN A 525 " --> pdb=" O ASP A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.627A pdb=" N LYS A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.643A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.920A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 removed outlier: 4.038A pdb=" N LYS A 634 " --> pdb=" O LYS A 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 630 through 634' Processing helix chain 'A' and resid 635 through 652 Processing helix chain 'A' and resid 674 through 685 removed outlier: 4.056A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 704 through 713 removed outlier: 4.438A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 736 removed outlier: 4.145A pdb=" N ASN A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 792 removed outlier: 3.580A pdb=" N TRP A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.675A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.925A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.860A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.885A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.846A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.783A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.880A pdb=" N ARG C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 257' Processing helix chain 'C' and resid 258 through 263 removed outlier: 4.118A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 286 through 296 removed outlier: 4.496A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.989A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.522A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.611A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.974A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.722A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 3.561A pdb=" N LEU A 107 " --> pdb=" O TYR A 658 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER A 158 " --> pdb=" O HIS A 657 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER A 431 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 382 Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA8, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.888A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.980A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.464A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 241 512 hydrogen bonds defined for protein. 1437 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.53 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1687 1.32 - 1.44: 2731 1.44 - 1.57: 5801 1.57 - 1.69: 6 1.69 - 1.81: 102 Bond restraints: 10327 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.450 0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.202 0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.463 0.062 2.10e-02 2.27e+03 8.60e+00 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.369 -0.040 1.40e-02 5.10e+03 8.33e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.33e+00 ... (remaining 10322 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 13543 2.38 - 4.76: 349 4.76 - 7.14: 45 7.14 - 9.51: 7 9.51 - 11.89: 4 Bond angle restraints: 13948 Sorted by residual: angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 109.81 11.89 1.80e+00 3.09e-01 4.37e+01 angle pdb=" CA TRP C 356 " pdb=" CB TRP C 356 " pdb=" CG TRP C 356 " ideal model delta sigma weight residual 113.60 122.80 -9.20 1.90e+00 2.77e-01 2.34e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.81 -4.81 1.10e+00 8.26e-01 1.91e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 102.06 8.04 1.90e+00 2.77e-01 1.79e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 118.21 4.19 1.00e+00 1.00e+00 1.75e+01 ... (remaining 13943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.17: 5978 27.17 - 54.34: 198 54.34 - 81.51: 41 81.51 - 108.69: 9 108.69 - 135.86: 4 Dihedral angle restraints: 6230 sinusoidal: 2564 harmonic: 3666 Sorted by residual: dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 75.86 -135.86 1 2.00e+01 2.50e-03 4.12e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 71.60 -131.60 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" O1B ADP A1902 " pdb=" O3A ADP A1902 " pdb=" PB ADP A1902 " pdb=" PA ADP A1902 " ideal model delta sinusoidal sigma weight residual -60.00 67.63 -127.64 1 2.00e+01 2.50e-03 3.87e+01 ... (remaining 6227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1165 0.059 - 0.118: 287 0.118 - 0.177: 61 0.177 - 0.236: 9 0.236 - 0.295: 2 Chirality restraints: 1524 Sorted by residual: chirality pdb=" CA TYR A 711 " pdb=" N TYR A 711 " pdb=" C TYR A 711 " pdb=" CB TYR A 711 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA HIS A 418 " pdb=" N HIS A 418 " pdb=" C HIS A 418 " pdb=" CB HIS A 418 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ARG A 213 " pdb=" N ARG A 213 " pdb=" C ARG A 213 " pdb=" CB ARG A 213 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1521 not shown) Planarity restraints: 1779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 28 " 0.133 9.50e-02 1.11e+02 7.79e-02 3.35e+01 pdb=" NE ARG C 28 " -0.041 2.00e-02 2.50e+03 pdb=" CZ ARG C 28 " 0.095 2.00e-02 2.50e+03 pdb=" NH1 ARG C 28 " -0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG C 28 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 677 " 0.140 9.50e-02 1.11e+02 7.83e-02 3.01e+01 pdb=" NE ARG A 677 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG A 677 " 0.090 2.00e-02 2.50e+03 pdb=" NH1 ARG A 677 " -0.032 2.00e-02 2.50e+03 pdb=" NH2 ARG A 677 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 477 " -0.001 2.00e-02 2.50e+03 3.42e-02 2.34e+01 pdb=" CG TYR A 477 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR A 477 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 477 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR A 477 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 477 " -0.049 2.00e-02 2.50e+03 pdb=" CZ TYR A 477 " -0.049 2.00e-02 2.50e+03 pdb=" OH TYR A 477 " 0.050 2.00e-02 2.50e+03 ... (remaining 1776 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 18 2.37 - 3.00: 5558 3.00 - 3.63: 14983 3.63 - 4.27: 22360 4.27 - 4.90: 37639 Nonbonded interactions: 80558 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.732 3.620 nonbonded pdb="MG MG A1901 " pdb=" O1B ADP A1902 " model vdw 1.947 2.170 nonbonded pdb=" OG1 THR A 170 " pdb="MG MG A1901 " model vdw 2.021 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.136 2.170 nonbonded pdb=" OH TYR A 528 " pdb=" O ALA A 547 " model vdw 2.162 3.040 ... (remaining 80553 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.010 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 10329 Z= 0.279 Angle : 0.936 11.894 13954 Z= 0.545 Chirality : 0.056 0.295 1524 Planarity : 0.009 0.117 1777 Dihedral : 15.861 135.857 3860 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.19 % Favored : 99.72 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.21), residues: 1224 helix: -1.69 (0.17), residues: 566 sheet: 0.17 (0.36), residues: 155 loop : 0.23 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP C 356 HIS 0.008 0.002 HIS B 132 PHE 0.031 0.003 PHE C 255 TYR 0.050 0.007 TYR A 477 ARG 0.097 0.013 ARG C 28 Details of bonding type rmsd link_TRANS : bond 0.00923 ( 2) link_TRANS : angle 4.22853 ( 6) hydrogen bonds : bond 0.15763 ( 510) hydrogen bonds : angle 7.48772 ( 1437) covalent geometry : bond 0.00605 (10327) covalent geometry : angle 0.93188 (13948) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.8082 (p0) cc_final: 0.7874 (p0) REVERT: A 790 MET cc_start: -0.0217 (ppp) cc_final: -0.0449 (ptm) REVERT: C 313 MET cc_start: 0.8525 (mmm) cc_final: 0.8321 (tpt) outliers start: 1 outliers final: 1 residues processed: 141 average time/residue: 0.2792 time to fit residues: 53.4867 Evaluate side-chains 80 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.7980 chunk 93 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 147 HIS A 264 GLN A 290 GLN A 354 HIS A 373 HIS A 398 ASN ** A 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 GLN A 755 GLN C 121 GLN C 161 HIS C 162 ASN C 371 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.072613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.052492 restraints weight = 38636.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.054376 restraints weight = 18514.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.055555 restraints weight = 11476.298| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10329 Z= 0.148 Angle : 0.687 10.139 13954 Z= 0.352 Chirality : 0.045 0.280 1524 Planarity : 0.004 0.046 1777 Dihedral : 10.313 133.990 1398 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 1.21 % Allowed : 5.76 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.23), residues: 1224 helix: 0.78 (0.21), residues: 587 sheet: 0.84 (0.38), residues: 150 loop : 0.56 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 484 HIS 0.004 0.001 HIS C 275 PHE 0.026 0.002 PHE C 223 TYR 0.014 0.002 TYR A 50 ARG 0.011 0.001 ARG A 152 Details of bonding type rmsd link_TRANS : bond 0.00240 ( 2) link_TRANS : angle 1.10654 ( 6) hydrogen bonds : bond 0.04131 ( 510) hydrogen bonds : angle 5.36068 ( 1437) covalent geometry : bond 0.00330 (10327) covalent geometry : angle 0.68656 (13948) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 PHE cc_start: 0.7045 (m-10) cc_final: 0.6653 (m-80) REVERT: B 120 MET cc_start: 0.7560 (mmp) cc_final: 0.6685 (mmm) REVERT: A 132 MET cc_start: 0.7521 (ppp) cc_final: 0.6341 (ppp) REVERT: A 788 MET cc_start: 0.5046 (ptp) cc_final: 0.4667 (mtt) REVERT: C 41 GLN cc_start: 0.8470 (tp-100) cc_final: 0.8231 (tm-30) REVERT: C 107 GLU cc_start: 0.7215 (tt0) cc_final: 0.6678 (tt0) REVERT: C 217 CYS cc_start: 0.8717 (m) cc_final: 0.8324 (m) REVERT: C 227 MET cc_start: 0.8612 (tpp) cc_final: 0.8300 (tpp) REVERT: C 313 MET cc_start: 0.8949 (mmm) cc_final: 0.8679 (tpt) outliers start: 13 outliers final: 6 residues processed: 116 average time/residue: 0.2263 time to fit residues: 37.8905 Evaluate side-chains 84 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 380 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 87 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.072149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.052049 restraints weight = 39165.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.053960 restraints weight = 18620.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.055199 restraints weight = 11447.336| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10329 Z= 0.145 Angle : 0.605 8.311 13954 Z= 0.307 Chirality : 0.042 0.181 1524 Planarity : 0.004 0.049 1777 Dihedral : 8.840 134.916 1397 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.30 % Allowed : 7.99 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.24), residues: 1224 helix: 1.35 (0.22), residues: 597 sheet: 1.00 (0.41), residues: 139 loop : 0.59 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 414 HIS 0.005 0.001 HIS C 275 PHE 0.014 0.001 PHE C 255 TYR 0.014 0.001 TYR A 259 ARG 0.007 0.000 ARG A 343 Details of bonding type rmsd link_TRANS : bond 0.00224 ( 2) link_TRANS : angle 1.11136 ( 6) hydrogen bonds : bond 0.03736 ( 510) hydrogen bonds : angle 4.96719 ( 1437) covalent geometry : bond 0.00325 (10327) covalent geometry : angle 0.60420 (13948) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 PHE cc_start: 0.3941 (t80) cc_final: 0.2997 (t80) REVERT: A 132 MET cc_start: 0.7477 (ppp) cc_final: 0.6958 (ppp) REVERT: A 788 MET cc_start: 0.5056 (ptp) cc_final: 0.4634 (mtt) REVERT: C 217 CYS cc_start: 0.8908 (m) cc_final: 0.8546 (m) REVERT: C 227 MET cc_start: 0.8581 (tpp) cc_final: 0.8144 (tpp) REVERT: C 241 GLU cc_start: 0.8162 (mp0) cc_final: 0.7899 (pm20) REVERT: C 299 MET cc_start: 0.8811 (mmm) cc_final: 0.8488 (mmm) outliers start: 14 outliers final: 7 residues processed: 97 average time/residue: 0.1981 time to fit residues: 29.0690 Evaluate side-chains 88 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 777 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 82 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 121 optimal weight: 0.4980 chunk 35 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.071533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.051432 restraints weight = 38812.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.053299 restraints weight = 18616.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.054541 restraints weight = 11521.769| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10329 Z= 0.153 Angle : 0.597 9.804 13954 Z= 0.298 Chirality : 0.042 0.179 1524 Planarity : 0.004 0.040 1777 Dihedral : 8.391 133.841 1397 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.02 % Allowed : 9.94 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1224 helix: 1.48 (0.22), residues: 600 sheet: 0.96 (0.41), residues: 139 loop : 0.51 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 79 HIS 0.005 0.001 HIS C 275 PHE 0.021 0.001 PHE B 12 TYR 0.013 0.001 TYR A 259 ARG 0.004 0.000 ARG A 152 Details of bonding type rmsd link_TRANS : bond 0.00212 ( 2) link_TRANS : angle 0.99721 ( 6) hydrogen bonds : bond 0.03583 ( 510) hydrogen bonds : angle 4.85306 ( 1437) covalent geometry : bond 0.00345 (10327) covalent geometry : angle 0.59706 (13948) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 PHE cc_start: 0.7800 (t80) cc_final: 0.7527 (t80) REVERT: B 140 ASN cc_start: 0.9531 (m-40) cc_final: 0.9002 (p0) REVERT: A 132 MET cc_start: 0.7673 (ppp) cc_final: 0.7111 (ppp) REVERT: A 788 MET cc_start: 0.5101 (ptp) cc_final: 0.4689 (mtt) REVERT: C 54 VAL cc_start: 0.9239 (t) cc_final: 0.8435 (m) REVERT: C 57 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8530 (pt0) REVERT: C 217 CYS cc_start: 0.8926 (m) cc_final: 0.8626 (m) REVERT: C 227 MET cc_start: 0.8572 (tpp) cc_final: 0.8284 (tpp) REVERT: C 241 GLU cc_start: 0.8151 (mp0) cc_final: 0.7883 (pm20) outliers start: 11 outliers final: 9 residues processed: 88 average time/residue: 0.2030 time to fit residues: 27.2617 Evaluate side-chains 81 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 671 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.071805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.051634 restraints weight = 38814.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.053545 restraints weight = 18547.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.054767 restraints weight = 11429.079| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10329 Z= 0.132 Angle : 0.579 8.815 13954 Z= 0.285 Chirality : 0.041 0.178 1524 Planarity : 0.003 0.040 1777 Dihedral : 8.061 130.066 1397 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.30 % Allowed : 10.77 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.25), residues: 1224 helix: 1.57 (0.22), residues: 607 sheet: 1.22 (0.40), residues: 149 loop : 0.43 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 484 HIS 0.010 0.001 HIS A 354 PHE 0.014 0.001 PHE B 12 TYR 0.012 0.001 TYR A 259 ARG 0.003 0.000 ARG A 343 Details of bonding type rmsd link_TRANS : bond 0.00204 ( 2) link_TRANS : angle 0.93026 ( 6) hydrogen bonds : bond 0.03369 ( 510) hydrogen bonds : angle 4.74676 ( 1437) covalent geometry : bond 0.00298 (10327) covalent geometry : angle 0.57879 (13948) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 140 ASN cc_start: 0.9566 (m-40) cc_final: 0.9049 (p0) REVERT: A 132 MET cc_start: 0.7636 (ppp) cc_final: 0.7065 (ppp) REVERT: A 788 MET cc_start: 0.5179 (ptp) cc_final: 0.4740 (mtt) REVERT: C 54 VAL cc_start: 0.9242 (t) cc_final: 0.8415 (m) REVERT: C 217 CYS cc_start: 0.8937 (m) cc_final: 0.8607 (m) REVERT: C 227 MET cc_start: 0.8573 (tpp) cc_final: 0.8141 (tpp) REVERT: C 241 GLU cc_start: 0.8137 (mp0) cc_final: 0.7876 (pm20) outliers start: 14 outliers final: 11 residues processed: 91 average time/residue: 0.2248 time to fit residues: 30.0311 Evaluate side-chains 82 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 111 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 41 optimal weight: 0.0670 chunk 36 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.072042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.051900 restraints weight = 38783.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.053816 restraints weight = 18607.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.055026 restraints weight = 11397.157| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10329 Z= 0.123 Angle : 0.582 9.363 13954 Z= 0.285 Chirality : 0.041 0.177 1524 Planarity : 0.003 0.038 1777 Dihedral : 7.813 126.127 1397 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.11 % Allowed : 11.33 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.24), residues: 1224 helix: 1.63 (0.22), residues: 603 sheet: 1.29 (0.40), residues: 154 loop : 0.31 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 484 HIS 0.007 0.001 HIS A 354 PHE 0.020 0.001 PHE B 19 TYR 0.011 0.001 TYR A 259 ARG 0.007 0.000 ARG A 343 Details of bonding type rmsd link_TRANS : bond 0.00199 ( 2) link_TRANS : angle 0.89772 ( 6) hydrogen bonds : bond 0.03271 ( 510) hydrogen bonds : angle 4.69322 ( 1437) covalent geometry : bond 0.00279 (10327) covalent geometry : angle 0.58196 (13948) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 788 MET cc_start: 0.5005 (ptp) cc_final: 0.4527 (mtt) REVERT: C 217 CYS cc_start: 0.8935 (m) cc_final: 0.8589 (m) REVERT: C 227 MET cc_start: 0.8579 (tpp) cc_final: 0.8177 (tpp) outliers start: 12 outliers final: 10 residues processed: 84 average time/residue: 0.2022 time to fit residues: 25.6373 Evaluate side-chains 80 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 107 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 119 optimal weight: 0.0970 chunk 103 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 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 = 0.3498 r_free = 0.3498 target = 0.072269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.052074 restraints weight = 38988.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.054007 restraints weight = 18626.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.055247 restraints weight = 11468.026| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10329 Z= 0.113 Angle : 0.580 10.085 13954 Z= 0.281 Chirality : 0.040 0.175 1524 Planarity : 0.003 0.039 1777 Dihedral : 7.537 120.842 1397 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.49 % Allowed : 11.70 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.24), residues: 1224 helix: 1.65 (0.22), residues: 608 sheet: 1.33 (0.40), residues: 153 loop : 0.30 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 484 HIS 0.004 0.001 HIS A 354 PHE 0.037 0.001 PHE B 12 TYR 0.009 0.001 TYR A 259 ARG 0.004 0.000 ARG A 343 Details of bonding type rmsd link_TRANS : bond 0.00200 ( 2) link_TRANS : angle 0.87525 ( 6) hydrogen bonds : bond 0.03163 ( 510) hydrogen bonds : angle 4.60105 ( 1437) covalent geometry : bond 0.00256 (10327) covalent geometry : angle 0.58005 (13948) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7371 (ppp) cc_final: 0.6621 (ppp) REVERT: A 500 GLU cc_start: 0.8326 (tt0) cc_final: 0.7942 (tm-30) REVERT: A 788 MET cc_start: 0.4989 (ptp) cc_final: 0.4329 (mtt) REVERT: C 217 CYS cc_start: 0.8901 (m) cc_final: 0.8540 (m) REVERT: C 227 MET cc_start: 0.8522 (tpp) cc_final: 0.8138 (tpp) outliers start: 16 outliers final: 10 residues processed: 85 average time/residue: 0.2025 time to fit residues: 26.5136 Evaluate side-chains 81 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 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: 124 random chunks: chunk 56 optimal weight: 0.0770 chunk 38 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 72 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 66 optimal weight: 0.0770 chunk 106 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.072654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.052500 restraints weight = 39144.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.054404 restraints weight = 18616.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.055631 restraints weight = 11421.284| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10329 Z= 0.105 Angle : 0.587 10.563 13954 Z= 0.281 Chirality : 0.040 0.173 1524 Planarity : 0.003 0.038 1777 Dihedral : 7.335 116.813 1397 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.30 % Allowed : 11.98 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.24), residues: 1224 helix: 1.66 (0.22), residues: 608 sheet: 1.35 (0.40), residues: 153 loop : 0.28 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 484 HIS 0.004 0.001 HIS A 354 PHE 0.035 0.001 PHE B 19 TYR 0.013 0.001 TYR A 787 ARG 0.004 0.000 ARG A 343 Details of bonding type rmsd link_TRANS : bond 0.00197 ( 2) link_TRANS : angle 0.86485 ( 6) hydrogen bonds : bond 0.03086 ( 510) hydrogen bonds : angle 4.54218 ( 1437) covalent geometry : bond 0.00236 (10327) covalent geometry : angle 0.58652 (13948) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 1.110 Fit side-chains REVERT: H 1 TRP cc_start: 0.8802 (m100) cc_final: 0.8225 (m100) REVERT: A 132 MET cc_start: 0.7350 (ppp) cc_final: 0.6569 (ppp) REVERT: A 484 TRP cc_start: 0.7243 (t60) cc_final: 0.6931 (t60) REVERT: A 500 GLU cc_start: 0.8302 (tt0) cc_final: 0.7920 (tm-30) REVERT: A 788 MET cc_start: 0.4777 (ptp) cc_final: 0.4290 (mtt) REVERT: C 217 CYS cc_start: 0.8876 (m) cc_final: 0.8523 (m) REVERT: C 227 MET cc_start: 0.8452 (tpp) cc_final: 0.8186 (tpp) outliers start: 14 outliers final: 10 residues processed: 87 average time/residue: 0.1911 time to fit residues: 25.7417 Evaluate side-chains 84 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 111 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 19 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 HIS C 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.071954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.051720 restraints weight = 38835.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.053644 restraints weight = 18640.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.054895 restraints weight = 11493.282| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10329 Z= 0.131 Angle : 0.611 11.009 13954 Z= 0.292 Chirality : 0.041 0.174 1524 Planarity : 0.003 0.039 1777 Dihedral : 7.277 114.741 1397 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.30 % Allowed : 12.07 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.24), residues: 1224 helix: 1.75 (0.22), residues: 604 sheet: 1.28 (0.40), residues: 154 loop : 0.28 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 484 HIS 0.004 0.001 HIS A 531 PHE 0.033 0.001 PHE B 19 TYR 0.017 0.001 TYR A 787 ARG 0.003 0.000 ARG A 343 Details of bonding type rmsd link_TRANS : bond 0.00217 ( 2) link_TRANS : angle 0.86345 ( 6) hydrogen bonds : bond 0.03214 ( 510) hydrogen bonds : angle 4.56975 ( 1437) covalent geometry : bond 0.00299 (10327) covalent geometry : angle 0.61121 (13948) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.5729 (m-10) cc_final: 0.5128 (m-10) REVERT: A 132 MET cc_start: 0.7257 (ppp) cc_final: 0.6441 (ppp) REVERT: A 500 GLU cc_start: 0.8325 (tt0) cc_final: 0.7929 (tm-30) REVERT: A 788 MET cc_start: 0.4781 (ptp) cc_final: 0.4234 (mtt) REVERT: C 217 CYS cc_start: 0.8909 (m) cc_final: 0.8573 (m) REVERT: C 227 MET cc_start: 0.8473 (tpp) cc_final: 0.8213 (tpp) outliers start: 14 outliers final: 11 residues processed: 85 average time/residue: 0.1906 time to fit residues: 25.1045 Evaluate side-chains 83 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 153 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 8 optimal weight: 8.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.071759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.051497 restraints weight = 39128.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.053419 restraints weight = 18831.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.054676 restraints weight = 11639.362| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10329 Z= 0.129 Angle : 0.616 11.410 13954 Z= 0.291 Chirality : 0.041 0.179 1524 Planarity : 0.003 0.038 1777 Dihedral : 7.237 115.247 1397 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.21 % Allowed : 12.26 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.24), residues: 1224 helix: 1.74 (0.22), residues: 604 sheet: 1.25 (0.40), residues: 154 loop : 0.25 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 484 HIS 0.004 0.001 HIS A 531 PHE 0.028 0.001 PHE B 19 TYR 0.013 0.001 TYR A 787 ARG 0.004 0.000 ARG B 64 Details of bonding type rmsd link_TRANS : bond 0.00215 ( 2) link_TRANS : angle 0.85262 ( 6) hydrogen bonds : bond 0.03199 ( 510) hydrogen bonds : angle 4.57340 ( 1437) covalent geometry : bond 0.00294 (10327) covalent geometry : angle 0.61613 (13948) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.5725 (m-10) cc_final: 0.5157 (m-10) REVERT: A 132 MET cc_start: 0.7267 (ppp) cc_final: 0.6453 (ppp) REVERT: A 500 GLU cc_start: 0.8379 (tt0) cc_final: 0.7957 (tm-30) REVERT: A 788 MET cc_start: 0.4780 (ptp) cc_final: 0.4212 (mtt) REVERT: C 217 CYS cc_start: 0.8905 (m) cc_final: 0.8598 (m) REVERT: C 227 MET cc_start: 0.8469 (tpp) cc_final: 0.8214 (tpp) outliers start: 13 outliers final: 13 residues processed: 84 average time/residue: 0.1919 time to fit residues: 24.9197 Evaluate side-chains 84 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 313 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 65 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS A 410 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 = 0.3468 r_free = 0.3468 target = 0.070832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.050589 restraints weight = 39179.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.052489 restraints weight = 18987.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.053724 restraints weight = 11749.672| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10329 Z= 0.165 Angle : 0.639 11.023 13954 Z= 0.304 Chirality : 0.041 0.204 1524 Planarity : 0.003 0.038 1777 Dihedral : 7.295 116.537 1397 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.21 % Allowed : 12.63 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.24), residues: 1224 helix: 1.72 (0.22), residues: 604 sheet: 1.18 (0.41), residues: 155 loop : 0.23 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 484 HIS 0.005 0.001 HIS A 531 PHE 0.025 0.001 PHE B 19 TYR 0.014 0.001 TYR A 259 ARG 0.005 0.000 ARG B 64 Details of bonding type rmsd link_TRANS : bond 0.00239 ( 2) link_TRANS : angle 0.85337 ( 6) hydrogen bonds : bond 0.03414 ( 510) hydrogen bonds : angle 4.65054 ( 1437) covalent geometry : bond 0.00372 (10327) covalent geometry : angle 0.63845 (13948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3784.61 seconds wall clock time: 66 minutes 15.35 seconds (3975.35 seconds total)