Starting phenix.real_space_refine on Fri Feb 14 18:06:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pm8_13524/02_2025/7pm8_13524.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pm8_13524/02_2025/7pm8_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7pm8_13524/02_2025/7pm8_13524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pm8_13524/02_2025/7pm8_13524.map" model { file = "/net/cci-nas-00/data/ceres_data/7pm8_13524/02_2025/7pm8_13524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pm8_13524/02_2025/7pm8_13524.cif" } resolution = 3.5 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 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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 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: "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, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} 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: 6.62, per 1000 atoms: 0.65 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: 2.80 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.25 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: 3.43 Time building geometry restraints manager: 3.12 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: 6090 31.71 - 63.42: 123 63.42 - 95.13: 38 95.13 - 126.84: 1 126.84 - 158.56: 2 Dihedral angle restraints: 6254 sinusoidal: 2572 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 6251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1091 0.047 - 0.094: 307 0.094 - 0.141: 109 0.141 - 0.188: 19 0.188 - 0.234: 4 Chirality restraints: 1530 Sorted by residual: 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 chirality pdb=" C2' ADP C 401 " pdb=" C1' ADP C 401 " pdb=" C3' ADP C 401 " pdb=" O2' ADP C 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.24e+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 1.11e+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: 2.430 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: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 26.560 Find NCS groups from input model: 0.110 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 10364 Z= 0.274 Angle : 0.881 11.918 14000 Z= 0.512 Chirality : 0.051 0.234 1530 Planarity : 0.009 0.169 1785 Dihedral : 15.707 158.556 3874 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 (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 (0.21), 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 TRP 0.029 0.003 TRP C 79 HIS 0.007 0.002 HIS C 275 PHE 0.034 0.002 PHE A 673 TYR 0.033 0.006 TYR A 113 ARG 0.091 0.010 ARG C 95 *********************** 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 : 1.162 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: 0.2686 time to fit residues: 58.0322 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 : 1.184 ------------------------------------------------------------------------------- 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 105 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 12 ASN C 161 HIS C 162 ASN C 173 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.071420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.051295 restraints weight = 40680.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.053149 restraints weight = 19257.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.054369 restraints weight = 11905.897| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10364 Z= 0.210 Angle : 0.679 7.824 14000 Z= 0.358 Chirality : 0.045 0.294 1530 Planarity : 0.005 0.049 1785 Dihedral : 10.101 169.400 1404 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.02 % Allowed : 6.48 % Favored : 92.51 % 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: 0.56 (0.23), residues: 1231 helix: 0.64 (0.20), residues: 603 sheet: 0.56 (0.40), residues: 145 loop : 0.17 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 1 HIS 0.016 0.001 HIS C 275 PHE 0.028 0.002 PHE B 19 TYR 0.034 0.002 TYR A 179 ARG 0.008 0.001 ARG A 152 *********************** 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 116 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 1.066 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: A 40 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8812 (mt) REVERT: A 135 MET cc_start: 0.8330 (mmm) cc_final: 0.7981 (mmm) REVERT: A 371 MET cc_start: 0.8401 (mmm) cc_final: 0.8175 (tpp) REVERT: A 476 GLU cc_start: 0.9061 (tp30) cc_final: 0.8826 (tp30) REVERT: A 783 MET cc_start: 0.8952 (mmp) cc_final: 0.8217 (mpp) REVERT: A 790 MET cc_start: 0.1102 (ptt) cc_final: 0.0116 (ttt) REVERT: B 29 TYR cc_start: 0.7914 (m-80) cc_final: 0.7611 (m-10) REVERT: B 120 MET cc_start: 0.5111 (mtt) cc_final: 0.4880 (mmm) REVERT: C 217 CYS cc_start: 0.8223 (m) cc_final: 0.7668 (m) REVERT: C 325 MET cc_start: 0.8864 (mmt) cc_final: 0.8403 (mmt) outliers start: 11 outliers final: 4 residues processed: 112 average time/residue: 0.2413 time to fit residues: 38.1006 Evaluate side-chains 87 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 662 ILE 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 111 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 84 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 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 = 0.3460 r_free = 0.3460 target = 0.069662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.049724 restraints weight = 41154.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.051507 restraints weight = 19699.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.052669 restraints weight = 12251.416| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10364 Z= 0.243 Angle : 0.636 12.016 14000 Z= 0.326 Chirality : 0.043 0.211 1530 Planarity : 0.004 0.051 1785 Dihedral : 9.281 170.064 1403 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.39 % Allowed : 7.86 % Favored : 90.75 % 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: 1.01 (0.24), residues: 1231 helix: 1.13 (0.21), residues: 610 sheet: 0.67 (0.41), residues: 145 loop : 0.23 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 79 HIS 0.012 0.001 HIS C 275 PHE 0.018 0.001 PHE A 360 TYR 0.025 0.001 TYR A 179 ARG 0.008 0.001 ARG C 95 *********************** 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 101 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8719 (mt) REVERT: A 135 MET cc_start: 0.8525 (mmm) cc_final: 0.8004 (mmm) REVERT: A 317 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8377 (tp) REVERT: A 323 MET cc_start: 0.8276 (mmp) cc_final: 0.8010 (tmm) REVERT: A 476 GLU cc_start: 0.9101 (tp30) cc_final: 0.8816 (tp30) REVERT: B 120 MET cc_start: 0.4888 (mtt) cc_final: 0.4670 (mmm) REVERT: C 81 ASP cc_start: 0.8578 (m-30) cc_final: 0.8059 (m-30) REVERT: C 123 MET cc_start: 0.8903 (tpp) cc_final: 0.8635 (mmm) REVERT: C 217 CYS cc_start: 0.8402 (m) cc_final: 0.7995 (m) outliers start: 15 outliers final: 3 residues processed: 96 average time/residue: 0.1932 time to fit residues: 28.5356 Evaluate side-chains 83 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 138 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 101 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 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 = 0.3463 r_free = 0.3463 target = 0.069825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.049751 restraints weight = 40707.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.051522 restraints weight = 19284.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.052676 restraints weight = 11975.340| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10364 Z= 0.218 Angle : 0.605 11.844 14000 Z= 0.305 Chirality : 0.042 0.217 1530 Planarity : 0.004 0.051 1785 Dihedral : 8.572 148.487 1403 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.11 % Allowed : 8.51 % Favored : 90.38 % 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: 1.16 (0.24), residues: 1231 helix: 1.29 (0.21), residues: 609 sheet: 0.71 (0.41), residues: 147 loop : 0.28 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 781 HIS 0.009 0.001 HIS C 275 PHE 0.020 0.001 PHE B 12 TYR 0.020 0.001 TYR A 179 ARG 0.006 0.000 ARG B 37 *********************** 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: 12 poor density : 83 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8787 (mt) REVERT: A 132 MET cc_start: 0.7530 (tmm) cc_final: 0.7211 (tmm) REVERT: A 135 MET cc_start: 0.8562 (mmm) cc_final: 0.8282 (mmm) REVERT: A 317 ILE cc_start: 0.8711 (mm) cc_final: 0.8349 (tp) REVERT: A 371 MET cc_start: 0.8464 (tpp) cc_final: 0.8165 (tpp) REVERT: A 476 GLU cc_start: 0.9092 (tp30) cc_final: 0.8835 (tp30) REVERT: C 81 ASP cc_start: 0.8564 (m-30) cc_final: 0.8042 (m-30) REVERT: C 123 MET cc_start: 0.8904 (tpp) cc_final: 0.8664 (mmm) REVERT: C 217 CYS cc_start: 0.8447 (m) cc_final: 0.8011 (m) outliers start: 12 outliers final: 6 residues processed: 91 average time/residue: 0.2026 time to fit residues: 28.2290 Evaluate side-chains 83 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 70 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3427 r_free = 0.3427 target = 0.068261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.048176 restraints weight = 41065.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.049937 restraints weight = 19662.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.051035 restraints weight = 12264.275| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10364 Z= 0.304 Angle : 0.630 10.736 14000 Z= 0.320 Chirality : 0.043 0.228 1530 Planarity : 0.004 0.051 1785 Dihedral : 8.122 119.919 1403 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.67 % Allowed : 8.97 % Favored : 89.36 % 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: 1.14 (0.24), residues: 1231 helix: 1.34 (0.21), residues: 609 sheet: 0.54 (0.41), residues: 147 loop : 0.22 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 781 HIS 0.008 0.001 HIS C 275 PHE 0.018 0.002 PHE B 12 TYR 0.019 0.001 TYR A 179 ARG 0.003 0.000 ARG A 155 *********************** 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 96 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8811 (mt) REVERT: A 135 MET cc_start: 0.8537 (mmm) cc_final: 0.8232 (mmm) REVERT: A 145 GLU cc_start: 0.8425 (tp30) cc_final: 0.8168 (tm-30) REVERT: A 323 MET cc_start: 0.8296 (mmp) cc_final: 0.8010 (tmm) REVERT: A 371 MET cc_start: 0.8492 (tpp) cc_final: 0.7921 (tpp) REVERT: C 81 ASP cc_start: 0.8502 (m-30) cc_final: 0.7995 (m-30) REVERT: C 123 MET cc_start: 0.8924 (tpp) cc_final: 0.8650 (mmm) REVERT: C 217 CYS cc_start: 0.8488 (m) cc_final: 0.8117 (m) outliers start: 18 outliers final: 9 residues processed: 92 average time/residue: 0.2050 time to fit residues: 28.5401 Evaluate side-chains 85 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 555 ASP Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 730 ASN 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.069137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.049077 restraints weight = 40704.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.050873 restraints weight = 19469.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.052034 restraints weight = 12092.465| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10364 Z= 0.203 Angle : 0.595 11.751 14000 Z= 0.299 Chirality : 0.042 0.227 1530 Planarity : 0.004 0.051 1785 Dihedral : 7.714 110.572 1403 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.39 % Allowed : 10.36 % Favored : 88.25 % 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: 1.27 (0.24), residues: 1231 helix: 1.47 (0.21), residues: 611 sheet: 0.51 (0.42), residues: 147 loop : 0.26 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 781 HIS 0.008 0.001 HIS C 275 PHE 0.021 0.001 PHE B 19 TYR 0.018 0.001 TYR A 179 ARG 0.004 0.000 ARG B 64 *********************** 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 101 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8679 (mt) REVERT: A 132 MET cc_start: 0.7772 (tmm) cc_final: 0.7527 (tmm) REVERT: A 135 MET cc_start: 0.8557 (mmm) cc_final: 0.8213 (mmm) REVERT: A 145 GLU cc_start: 0.8438 (tp30) cc_final: 0.8153 (tm-30) REVERT: A 371 MET cc_start: 0.8513 (tpp) cc_final: 0.7912 (tpp) REVERT: A 476 GLU cc_start: 0.9109 (tp30) cc_final: 0.8865 (tp30) REVERT: A 515 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7569 (mtt) REVERT: C 81 ASP cc_start: 0.8503 (m-30) cc_final: 0.8018 (m-30) REVERT: C 217 CYS cc_start: 0.8517 (m) cc_final: 0.8100 (m) REVERT: C 325 MET cc_start: 0.8872 (mmt) cc_final: 0.8514 (mmt) outliers start: 15 outliers final: 8 residues processed: 97 average time/residue: 0.1986 time to fit residues: 28.9977 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 : 1.214 ------------------------------------------------------------------------------- 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 577 ILE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 119 optimal weight: 0.8980 chunk 55 optimal weight: 0.3980 chunk 96 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 58 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.069632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.049478 restraints weight = 41306.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.051278 restraints weight = 19513.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.052442 restraints weight = 12085.030| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10364 Z= 0.181 Angle : 0.598 12.620 14000 Z= 0.297 Chirality : 0.041 0.212 1530 Planarity : 0.004 0.050 1785 Dihedral : 7.405 103.565 1403 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.20 % Allowed : 11.10 % Favored : 87.70 % 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: 1.38 (0.25), residues: 1231 helix: 1.58 (0.22), residues: 609 sheet: 0.63 (0.42), residues: 145 loop : 0.28 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 781 HIS 0.007 0.001 HIS C 275 PHE 0.020 0.001 PHE A 360 TYR 0.015 0.001 TYR A 179 ARG 0.009 0.000 ARG B 64 *********************** 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 100 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8557 (mmm) cc_final: 0.8189 (mmm) REVERT: A 145 GLU cc_start: 0.8468 (tp30) cc_final: 0.8187 (tm-30) REVERT: A 323 MET cc_start: 0.8206 (mmp) cc_final: 0.7955 (tmm) REVERT: A 371 MET cc_start: 0.8512 (tpp) cc_final: 0.7935 (tpp) REVERT: A 476 GLU cc_start: 0.9106 (tp30) cc_final: 0.8859 (tp30) REVERT: A 515 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7543 (mtt) REVERT: A 689 GLU cc_start: 0.8604 (tp30) cc_final: 0.8393 (tp30) REVERT: B 36 MET cc_start: 0.7344 (mmt) cc_final: 0.7125 (mmt) REVERT: C 81 ASP cc_start: 0.8428 (m-30) cc_final: 0.7969 (m-30) REVERT: C 217 CYS cc_start: 0.8476 (m) cc_final: 0.8051 (m) REVERT: C 325 MET cc_start: 0.8860 (mmt) cc_final: 0.8501 (mmt) outliers start: 13 outliers final: 8 residues processed: 97 average time/residue: 0.2155 time to fit residues: 31.5454 Evaluate side-chains 93 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS 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 735 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.0870 chunk 87 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 85 optimal weight: 0.0470 chunk 61 optimal weight: 0.6980 chunk 13 optimal weight: 0.0470 chunk 82 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 ASN ** 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 = 0.3477 r_free = 0.3477 target = 0.070335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.050235 restraints weight = 40823.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.052059 restraints weight = 19293.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.053227 restraints weight = 11919.307| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10364 Z= 0.158 Angle : 0.603 14.458 14000 Z= 0.295 Chirality : 0.041 0.208 1530 Planarity : 0.004 0.046 1785 Dihedral : 7.139 97.418 1403 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.48 % Allowed : 11.01 % Favored : 87.51 % 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: 1.53 (0.25), residues: 1231 helix: 1.73 (0.22), residues: 603 sheet: 0.63 (0.42), residues: 151 loop : 0.35 (0.31), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 781 HIS 0.006 0.001 HIS C 275 PHE 0.030 0.001 PHE B 12 TYR 0.014 0.001 TYR A 179 ARG 0.009 0.000 ARG A 712 *********************** 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 105 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8535 (mmm) cc_final: 0.8144 (mmm) REVERT: A 145 GLU cc_start: 0.8497 (tp30) cc_final: 0.8205 (tm-30) REVERT: A 323 MET cc_start: 0.8251 (mmp) cc_final: 0.7945 (tmm) REVERT: A 371 MET cc_start: 0.8501 (tpp) cc_final: 0.7933 (tpp) REVERT: A 476 GLU cc_start: 0.9125 (tp30) cc_final: 0.8874 (tp30) REVERT: A 515 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7537 (mtt) REVERT: B 36 MET cc_start: 0.7480 (mmt) cc_final: 0.7258 (mmt) REVERT: C 81 ASP cc_start: 0.8414 (m-30) cc_final: 0.7973 (m-30) REVERT: C 217 CYS cc_start: 0.8402 (m) cc_final: 0.7839 (m) REVERT: C 325 MET cc_start: 0.8851 (mmt) cc_final: 0.8475 (mmt) outliers start: 16 outliers final: 8 residues processed: 102 average time/residue: 0.2020 time to fit residues: 31.5243 Evaluate side-chains 94 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 27 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 42 optimal weight: 0.0870 chunk 76 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 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 = 0.3470 r_free = 0.3470 target = 0.069982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.049735 restraints weight = 40780.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.051539 restraints weight = 19385.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.052703 restraints weight = 12018.555| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10364 Z= 0.196 Angle : 0.612 12.823 14000 Z= 0.301 Chirality : 0.041 0.208 1530 Planarity : 0.004 0.047 1785 Dihedral : 7.082 96.622 1403 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.93 % Allowed : 11.75 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.45 (0.25), residues: 1231 helix: 1.70 (0.22), residues: 608 sheet: 0.50 (0.42), residues: 151 loop : 0.28 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 781 HIS 0.018 0.001 HIS A 418 PHE 0.031 0.002 PHE B 12 TYR 0.026 0.001 TYR A 179 ARG 0.004 0.000 ARG A 155 *********************** 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: 10 poor density : 85 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7542 (tmm) cc_final: 0.7198 (tmm) REVERT: A 135 MET cc_start: 0.8518 (mmm) cc_final: 0.8111 (mmm) REVERT: A 145 GLU cc_start: 0.8496 (tp30) cc_final: 0.8205 (tm-30) REVERT: A 323 MET cc_start: 0.8246 (mmp) cc_final: 0.7894 (tmm) REVERT: A 339 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8195 (mm-30) REVERT: A 371 MET cc_start: 0.8492 (tpp) cc_final: 0.7928 (tpp) REVERT: A 515 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7507 (mtt) REVERT: C 81 ASP cc_start: 0.8392 (m-30) cc_final: 0.7955 (m-30) REVERT: C 217 CYS cc_start: 0.8459 (m) cc_final: 0.8033 (m) REVERT: C 325 MET cc_start: 0.8853 (mmt) cc_final: 0.8480 (mmt) outliers start: 10 outliers final: 8 residues processed: 91 average time/residue: 0.1950 time to fit residues: 27.0787 Evaluate side-chains 91 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 577 ILE 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 111 HIS Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain C residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 76 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.069832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.049595 restraints weight = 40821.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.051376 restraints weight = 19432.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.052531 restraints weight = 12082.664| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10364 Z= 0.197 Angle : 0.619 12.021 14000 Z= 0.306 Chirality : 0.042 0.210 1530 Planarity : 0.004 0.046 1785 Dihedral : 7.022 96.694 1403 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.02 % Allowed : 11.93 % Favored : 87.05 % 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: 1.40 (0.25), residues: 1231 helix: 1.66 (0.22), residues: 608 sheet: 0.51 (0.42), residues: 151 loop : 0.23 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 781 HIS 0.012 0.001 HIS A 418 PHE 0.037 0.001 PHE B 12 TYR 0.020 0.001 TYR A 179 ARG 0.005 0.000 ARG B 64 ********************** 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 93 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7493 (tmm) cc_final: 0.7171 (tmm) REVERT: A 135 MET cc_start: 0.8516 (mmm) cc_final: 0.8286 (mmm) REVERT: A 145 GLU cc_start: 0.8477 (tp30) cc_final: 0.8204 (tm-30) REVERT: A 323 MET cc_start: 0.8248 (mmp) cc_final: 0.7881 (tmm) REVERT: A 339 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8175 (mm-30) REVERT: A 371 MET cc_start: 0.8501 (tpp) cc_final: 0.7937 (tpp) REVERT: A 515 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7509 (mtt) REVERT: B 36 MET cc_start: 0.7524 (mmt) cc_final: 0.7164 (mmt) REVERT: C 81 ASP cc_start: 0.8389 (m-30) cc_final: 0.7955 (m-30) REVERT: C 217 CYS cc_start: 0.8402 (m) cc_final: 0.7997 (m) REVERT: C 325 MET cc_start: 0.8853 (mmt) cc_final: 0.8477 (mmt) outliers start: 11 outliers final: 10 residues processed: 90 average time/residue: 0.2032 time to fit residues: 27.9032 Evaluate side-chains 90 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS 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 671 PHE Chi-restraints excluded: chain A residue 781 TRP Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain C residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 16 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 83 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 65 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 HIS ** 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 = 0.3475 r_free = 0.3475 target = 0.070141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.049924 restraints weight = 40463.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.051703 restraints weight = 19312.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.052852 restraints weight = 12021.741| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10364 Z= 0.186 Angle : 0.604 12.023 14000 Z= 0.298 Chirality : 0.041 0.208 1530 Planarity : 0.004 0.046 1785 Dihedral : 6.874 94.144 1403 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.02 % Allowed : 11.93 % Favored : 87.05 % 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: 1.38 (0.25), residues: 1231 helix: 1.64 (0.22), residues: 607 sheet: 0.49 (0.42), residues: 151 loop : 0.24 (0.31), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 781 HIS 0.012 0.001 HIS A 418 PHE 0.033 0.001 PHE B 12 TYR 0.021 0.001 TYR A 179 ARG 0.005 0.000 ARG B 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3328.67 seconds wall clock time: 60 minutes 48.62 seconds (3648.62 seconds total)