Starting phenix.real_space_refine on Fri Feb 14 05:36:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vqt_21356/02_2025/6vqt_21356.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vqt_21356/02_2025/6vqt_21356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vqt_21356/02_2025/6vqt_21356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vqt_21356/02_2025/6vqt_21356.map" model { file = "/net/cci-nas-00/data/ceres_data/6vqt_21356/02_2025/6vqt_21356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vqt_21356/02_2025/6vqt_21356.cif" } resolution = 3.03 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= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 657 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians V 2 8.30 5 P 4 5.49 5 Mg 2 5.21 5 S 24 5.16 5 C 5822 2.51 5 N 1620 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 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: 9144 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4539 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 15, 'TRANS': 568} Chain: "B" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4539 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 15, 'TRANS': 568} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 38 Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.84, per 1000 atoms: 0.64 Number of scatterers: 9144 At special positions: 0 Unit cell: (72.437, 91.1854, 141.465, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 2 22.97 S 24 16.00 P 4 15.00 Mg 2 11.99 O 1670 8.00 N 1620 7.00 C 5822 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 883.3 milliseconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 4 sheets defined 72.1% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 15 through 28 Proline residue: A 25 - end of helix removed outlier: 3.662A pdb=" N TRP A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 68 removed outlier: 3.511A pdb=" N ARG A 36 " --> pdb=" O ASN A 32 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Proline residue: A 57 - end of helix removed outlier: 3.542A pdb=" N THR A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 127 removed outlier: 5.040A pdb=" N ARG A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL A 108 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 109 " --> pdb=" O PHE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 removed outlier: 4.219A pdb=" N ALA A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 161 removed outlier: 3.593A pdb=" N VAL A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 180 Processing helix chain 'A' and resid 182 through 230 removed outlier: 4.335A pdb=" N HIS A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU A 209 " --> pdb=" O TRP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 239 through 293 removed outlier: 3.846A pdb=" N ALA A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 319 Proline residue: A 314 - end of helix removed outlier: 3.762A pdb=" N LEU A 318 " --> pdb=" O PRO A 314 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 341 removed outlier: 3.535A pdb=" N THR A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 408 removed outlier: 3.895A pdb=" N ALA A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 450 through 457 Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 499 through 515 Processing helix chain 'A' and resid 529 through 544 Processing helix chain 'A' and resid 555 through 560 removed outlier: 3.591A pdb=" N ALA A 560 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 587 through 598 Processing helix chain 'B' and resid 16 through 28 Proline residue: B 25 - end of helix removed outlier: 3.550A pdb=" N TRP B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 68 Proline residue: B 57 - end of helix removed outlier: 3.507A pdb=" N MET B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 127 removed outlier: 3.503A pdb=" N VAL B 95 " --> pdb=" O ARG B 91 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ARG B 107 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N VAL B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY B 109 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 removed outlier: 4.151A pdb=" N HIS B 132 " --> pdb=" O SER B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 161 removed outlier: 3.741A pdb=" N VAL B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 180 Processing helix chain 'B' and resid 182 through 230 removed outlier: 4.103A pdb=" N HIS B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU B 209 " --> pdb=" O TRP B 205 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 239 through 293 removed outlier: 3.771A pdb=" N ALA B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 319 removed outlier: 3.962A pdb=" N VAL B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) Proline residue: B 314 - end of helix removed outlier: 3.703A pdb=" N MET B 317 " --> pdb=" O ARG B 313 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU B 318 " --> pdb=" O PRO B 314 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 341 removed outlier: 3.572A pdb=" N THR B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 408 removed outlier: 4.365A pdb=" N ALA B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 450 through 457 Processing helix chain 'B' and resid 463 through 474 Processing helix chain 'B' and resid 476 through 482 Processing helix chain 'B' and resid 485 through 489 Processing helix chain 'B' and resid 499 through 515 Processing helix chain 'B' and resid 529 through 544 Processing helix chain 'B' and resid 555 through 560 removed outlier: 3.586A pdb=" N ALA B 560 " --> pdb=" O SER B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 586 Processing helix chain 'B' and resid 587 through 598 Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 384 removed outlier: 7.217A pdb=" N HIS A 378 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL A 367 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU A 380 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN A 365 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL A 366 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLU A 415 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 437 through 440 removed outlier: 6.563A pdb=" N LEU A 519 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE A 552 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE A 521 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 390 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG A 389 " --> pdb=" O THR A 564 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LEU A 566 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA A 391 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU A 568 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 393 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE A 565 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLN A 576 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL A 567 " --> pdb=" O ALA A 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 377 through 384 removed outlier: 7.449A pdb=" N HIS B 378 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL B 367 " --> pdb=" O HIS B 378 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU B 380 " --> pdb=" O ASN B 365 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN B 365 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL B 366 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLU B 415 " --> pdb=" O VAL B 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 437 through 440 removed outlier: 6.676A pdb=" N GLY B 438 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASP B 522 " --> pdb=" O GLY B 438 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B 440 " --> pdb=" O ASP B 522 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 519 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE B 552 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE B 521 " --> pdb=" O ILE B 552 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL B 390 " --> pdb=" O SER B 551 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ARG B 389 " --> pdb=" O THR B 564 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU B 566 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA B 391 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU B 568 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL B 393 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ILE B 565 " --> pdb=" O GLN B 576 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLN B 576 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL B 567 " --> pdb=" O ALA B 574 " (cutoff:3.500A) 629 hydrogen bonds defined for protein. 1839 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3021 1.34 - 1.46: 1165 1.46 - 1.57: 5062 1.57 - 1.69: 8 1.69 - 1.80: 56 Bond restraints: 9312 Sorted by residual: bond pdb=" C1' ADP B 701 " pdb=" C2' ADP B 701 " ideal model delta sigma weight residual 1.524 1.293 0.231 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C1' ADP A 701 " pdb=" C2' ADP A 701 " ideal model delta sigma weight residual 1.524 1.293 0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C1' ADP A 701 " pdb=" O4' ADP A 701 " ideal model delta sigma weight residual 1.426 1.624 -0.198 2.00e-02 2.50e+03 9.77e+01 bond pdb=" C1' ADP B 701 " pdb=" O4' ADP B 701 " ideal model delta sigma weight residual 1.426 1.623 -0.197 2.00e-02 2.50e+03 9.69e+01 bond pdb=" C4 ADP B 701 " pdb=" C5 ADP B 701 " ideal model delta sigma weight residual 1.490 1.335 0.155 2.00e-02 2.50e+03 6.01e+01 ... (remaining 9307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 12457 3.36 - 6.72: 168 6.72 - 10.08: 15 10.08 - 13.44: 8 13.44 - 16.79: 14 Bond angle restraints: 12662 Sorted by residual: angle pdb=" N VAL B 321 " pdb=" CA VAL B 321 " pdb=" C VAL B 321 " ideal model delta sigma weight residual 113.20 105.73 7.47 9.60e-01 1.09e+00 6.05e+01 angle pdb=" O2 VO4 A 702 " pdb=" V VO4 A 702 " pdb=" O4 VO4 A 702 " ideal model delta sigma weight residual 109.47 126.26 -16.79 3.00e+00 1.11e-01 3.13e+01 angle pdb=" O3 VO4 A 702 " pdb=" V VO4 A 702 " pdb=" O4 VO4 A 702 " ideal model delta sigma weight residual 109.47 126.16 -16.68 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O3 VO4 A 704 " pdb=" V VO4 A 704 " pdb=" O4 VO4 A 704 " ideal model delta sigma weight residual 109.47 126.07 -16.59 3.00e+00 1.11e-01 3.06e+01 angle pdb=" O2 VO4 A 704 " pdb=" V VO4 A 704 " pdb=" O4 VO4 A 704 " ideal model delta sigma weight residual 109.47 125.57 -16.10 3.00e+00 1.11e-01 2.88e+01 ... (remaining 12657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.78: 5270 30.78 - 61.57: 216 61.57 - 92.35: 21 92.35 - 123.14: 1 123.14 - 153.92: 2 Dihedral angle restraints: 5510 sinusoidal: 2144 harmonic: 3366 Sorted by residual: dihedral pdb=" C5' ADP B 701 " pdb=" O5' ADP B 701 " pdb=" PA ADP B 701 " pdb=" O2A ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 93.92 -153.92 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" O1B ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PB ADP B 701 " pdb=" PA ADP B 701 " ideal model delta sinusoidal sigma weight residual 300.00 170.92 129.07 1 2.00e+01 2.50e-03 3.91e+01 dihedral pdb=" C5' ADP A 701 " pdb=" O5' ADP A 701 " pdb=" PA ADP A 701 " pdb=" O2A ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 62.49 -122.49 1 2.00e+01 2.50e-03 3.69e+01 ... (remaining 5507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.187: 1480 0.187 - 0.375: 2 0.375 - 0.562: 0 0.562 - 0.749: 0 0.749 - 0.936: 2 Chirality restraints: 1484 Sorted by residual: chirality pdb=" V VO4 A 704 " pdb=" O1 VO4 A 704 " pdb=" O2 VO4 A 704 " pdb=" O4 VO4 A 704 " both_signs ideal model delta sigma weight residual True 5.36 -4.43 0.94 2.00e-01 2.50e+01 2.19e+01 chirality pdb=" V VO4 A 702 " pdb=" O1 VO4 A 702 " pdb=" O2 VO4 A 702 " pdb=" O4 VO4 A 702 " both_signs ideal model delta sigma weight residual True 5.36 4.44 0.92 2.00e-01 2.50e+01 2.14e+01 chirality pdb=" CG LEU B 582 " pdb=" CB LEU B 582 " pdb=" CD1 LEU B 582 " pdb=" CD2 LEU B 582 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1481 not shown) Planarity restraints: 1602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 74 " 0.053 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO B 75 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 75 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 75 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 401 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.53e+00 pdb=" C SER A 401 " -0.051 2.00e-02 2.50e+03 pdb=" O SER A 401 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 402 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 313 " 0.044 5.00e-02 4.00e+02 6.61e-02 7.00e+00 pdb=" N PRO B 314 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 314 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 314 " 0.037 5.00e-02 4.00e+02 ... (remaining 1599 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 23 2.37 - 3.00: 5304 3.00 - 3.63: 13339 3.63 - 4.27: 18479 4.27 - 4.90: 30362 Nonbonded interactions: 67507 Sorted by model distance: nonbonded pdb=" V VO4 A 704 " pdb="MG MG B 702 " model vdw 1.733 2.180 nonbonded pdb=" O2B ADP B 701 " pdb="MG MG B 702 " model vdw 1.891 2.170 nonbonded pdb=" O4 VO4 A 704 " pdb="MG MG B 702 " model vdw 1.895 2.170 nonbonded pdb=" O3B ADP A 701 " pdb="MG MG A 703 " model vdw 1.920 2.170 nonbonded pdb=" O2 VO4 A 704 " pdb="MG MG B 702 " model vdw 1.969 2.170 ... (remaining 67502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 598 or resid 701)) selection = (chain 'B' and (resid 15 through 598 or resid 701)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.760 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 : 0.009 0.231 9312 Z= 0.620 Angle : 1.151 16.795 12662 Z= 0.653 Chirality : 0.061 0.936 1484 Planarity : 0.006 0.080 1602 Dihedral : 16.315 153.919 3346 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.94 % Allowed : 13.41 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.39 (0.23), residues: 1164 helix: 1.65 (0.16), residues: 760 sheet: 0.63 (0.54), residues: 78 loop : -0.68 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 177 HIS 0.005 0.002 HIS A 115 PHE 0.020 0.002 PHE B 58 TYR 0.025 0.002 TYR B 289 ARG 0.013 0.002 ARG A 434 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 115 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8924 (tp) outliers start: 46 outliers final: 18 residues processed: 158 average time/residue: 0.2405 time to fit residues: 50.9827 Evaluate side-chains 98 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 205 TRP Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 342 HIS Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 525 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 32 ASN A 208 HIS A 263 ASN A 293 GLN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN A 570 GLN B 18 GLN B 74 GLN B 161 ASN B 293 GLN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN B 442 GLN B 504 GLN B 570 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.063250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.054403 restraints weight = 42154.608| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 5.30 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9312 Z= 0.219 Angle : 0.683 10.101 12662 Z= 0.357 Chirality : 0.042 0.180 1484 Planarity : 0.005 0.064 1602 Dihedral : 7.771 108.443 1351 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.47 % Allowed : 18.03 % Favored : 79.51 % 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: 2.68 (0.24), residues: 1164 helix: 2.70 (0.17), residues: 764 sheet: 0.84 (0.53), residues: 80 loop : -0.32 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 205 HIS 0.004 0.001 HIS B 208 PHE 0.017 0.001 PHE B 58 TYR 0.009 0.001 TYR A 87 ARG 0.006 0.001 ARG B 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 213 MET cc_start: 0.8799 (ttp) cc_final: 0.8470 (ttt) REVERT: A 316 ASP cc_start: 0.9343 (m-30) cc_final: 0.9117 (t0) REVERT: A 371 ASP cc_start: 0.8492 (m-30) cc_final: 0.7851 (t0) REVERT: A 412 ASP cc_start: 0.9165 (p0) cc_final: 0.8956 (p0) REVERT: B 157 PHE cc_start: 0.9038 (m-80) cc_final: 0.8823 (m-80) REVERT: B 206 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7502 (ttp80) REVERT: B 213 MET cc_start: 0.8735 (ttt) cc_final: 0.8508 (ttt) REVERT: B 320 MET cc_start: 0.9284 (ptp) cc_final: 0.8984 (ptp) REVERT: B 371 ASP cc_start: 0.8186 (t0) cc_final: 0.7963 (t0) REVERT: B 419 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8869 (pp) outliers start: 23 outliers final: 16 residues processed: 108 average time/residue: 0.2343 time to fit residues: 35.3928 Evaluate side-chains 93 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 342 HIS Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 554 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 11 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 99 optimal weight: 0.3980 chunk 6 optimal weight: 7.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.058972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.050395 restraints weight = 44136.233| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 5.31 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 9312 Z= 0.331 Angle : 0.684 10.250 12662 Z= 0.362 Chirality : 0.042 0.197 1484 Planarity : 0.005 0.042 1602 Dihedral : 7.151 102.857 1335 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.40 % Allowed : 18.24 % Favored : 77.36 % 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: 2.46 (0.24), residues: 1164 helix: 2.49 (0.18), residues: 764 sheet: 0.70 (0.52), residues: 80 loop : -0.25 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 177 HIS 0.003 0.001 HIS A 579 PHE 0.034 0.002 PHE B 312 TYR 0.012 0.001 TYR B 289 ARG 0.006 0.001 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 80 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 146 ARG cc_start: 0.9075 (mmm-85) cc_final: 0.8859 (tpp80) REVERT: A 157 PHE cc_start: 0.9108 (m-80) cc_final: 0.8661 (t80) REVERT: B 175 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8764 (tp) REVERT: B 213 MET cc_start: 0.8817 (ttt) cc_final: 0.8511 (ttt) REVERT: B 371 ASP cc_start: 0.8451 (t0) cc_final: 0.8107 (t0) REVERT: B 419 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8921 (pp) outliers start: 41 outliers final: 29 residues processed: 111 average time/residue: 0.1993 time to fit residues: 33.3168 Evaluate side-chains 102 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 71 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 554 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 111 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 125 HIS A 179 ASN B 99 ASN B 208 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.062347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.053411 restraints weight = 42131.035| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 5.36 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9312 Z= 0.172 Angle : 0.602 10.208 12662 Z= 0.305 Chirality : 0.040 0.193 1484 Planarity : 0.004 0.040 1602 Dihedral : 6.411 95.890 1330 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.86 % Allowed : 20.82 % Favored : 75.32 % 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: 2.74 (0.24), residues: 1164 helix: 2.74 (0.18), residues: 762 sheet: 0.75 (0.52), residues: 80 loop : -0.22 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 177 HIS 0.002 0.001 HIS A 342 PHE 0.029 0.001 PHE B 312 TYR 0.009 0.001 TYR A 87 ARG 0.009 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 82 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.9070 (m-80) cc_final: 0.8463 (t80) REVERT: A 284 MET cc_start: 0.7102 (tpp) cc_final: 0.6860 (tpp) REVERT: A 371 ASP cc_start: 0.8649 (m-30) cc_final: 0.8160 (t70) REVERT: B 157 PHE cc_start: 0.8970 (m-80) cc_final: 0.8507 (t80) REVERT: B 175 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8659 (tp) REVERT: B 213 MET cc_start: 0.8732 (ttt) cc_final: 0.8437 (ttt) REVERT: B 297 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8163 (t) REVERT: B 371 ASP cc_start: 0.8435 (t0) cc_final: 0.8003 (t0) REVERT: B 466 GLU cc_start: 0.9367 (OUTLIER) cc_final: 0.8969 (mp0) outliers start: 36 outliers final: 22 residues processed: 114 average time/residue: 0.1734 time to fit residues: 30.4301 Evaluate side-chains 99 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 342 HIS Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 525 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 32 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 chunk 98 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 277 ASN B 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.061837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.052999 restraints weight = 42701.677| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 5.35 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9312 Z= 0.191 Angle : 0.600 10.666 12662 Z= 0.301 Chirality : 0.039 0.205 1484 Planarity : 0.003 0.039 1602 Dihedral : 6.221 100.768 1328 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.86 % Allowed : 21.14 % Favored : 75.00 % 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: 2.81 (0.25), residues: 1164 helix: 2.78 (0.18), residues: 762 sheet: 0.83 (0.53), residues: 80 loop : -0.17 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 177 HIS 0.008 0.001 HIS B 208 PHE 0.019 0.001 PHE B 312 TYR 0.009 0.001 TYR A 87 ARG 0.005 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 76 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.8966 (m-80) cc_final: 0.8475 (t80) REVERT: A 206 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8009 (ttp80) REVERT: A 284 MET cc_start: 0.6891 (tpp) cc_final: 0.6538 (tpp) REVERT: A 320 MET cc_start: 0.9147 (ptp) cc_final: 0.8773 (pmm) REVERT: A 371 ASP cc_start: 0.8699 (m-30) cc_final: 0.8181 (t70) REVERT: B 157 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.8575 (t80) REVERT: B 175 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8689 (tp) REVERT: B 213 MET cc_start: 0.8757 (ttt) cc_final: 0.8440 (ttt) REVERT: B 232 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8918 (tp30) REVERT: B 297 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8194 (t) REVERT: B 371 ASP cc_start: 0.8534 (t0) cc_final: 0.8055 (t0) REVERT: B 466 GLU cc_start: 0.9363 (OUTLIER) cc_final: 0.8988 (mp0) outliers start: 36 outliers final: 28 residues processed: 105 average time/residue: 0.1654 time to fit residues: 26.2043 Evaluate side-chains 107 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 342 HIS Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 554 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 113 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.059952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.051220 restraints weight = 43466.798| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 5.32 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9312 Z= 0.269 Angle : 0.623 10.848 12662 Z= 0.319 Chirality : 0.039 0.203 1484 Planarity : 0.004 0.037 1602 Dihedral : 6.257 102.848 1328 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.61 % Allowed : 20.82 % Favored : 74.57 % 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: 2.69 (0.25), residues: 1164 helix: 2.69 (0.18), residues: 762 sheet: 0.70 (0.52), residues: 80 loop : -0.21 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 177 HIS 0.031 0.002 HIS A 125 PHE 0.019 0.001 PHE A 312 TYR 0.010 0.001 TYR B 289 ARG 0.004 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 78 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.8978 (m-80) cc_final: 0.8487 (t80) REVERT: A 206 ARG cc_start: 0.8569 (ttp80) cc_final: 0.8078 (ttp80) REVERT: A 213 MET cc_start: 0.8722 (ttp) cc_final: 0.8336 (ttm) REVERT: A 320 MET cc_start: 0.9171 (ptp) cc_final: 0.8782 (pmm) REVERT: B 157 PHE cc_start: 0.8994 (m-80) cc_final: 0.8568 (t80) REVERT: B 175 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8728 (tp) REVERT: B 213 MET cc_start: 0.8771 (ttt) cc_final: 0.8480 (ttt) REVERT: B 232 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8916 (tp30) REVERT: B 297 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8263 (t) REVERT: B 371 ASP cc_start: 0.8674 (t0) cc_final: 0.8227 (t0) REVERT: B 466 GLU cc_start: 0.9363 (OUTLIER) cc_final: 0.8995 (mp0) outliers start: 43 outliers final: 35 residues processed: 114 average time/residue: 0.1689 time to fit residues: 29.5424 Evaluate side-chains 114 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 76 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 342 HIS Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 554 HIS Chi-restraints excluded: chain B residue 568 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 112 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 504 GLN B 208 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.058116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.049398 restraints weight = 43941.485| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 5.39 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 9312 Z= 0.318 Angle : 0.666 10.699 12662 Z= 0.344 Chirality : 0.040 0.169 1484 Planarity : 0.004 0.035 1602 Dihedral : 6.340 102.056 1328 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 5.79 % Allowed : 20.71 % Favored : 73.50 % 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: 2.40 (0.25), residues: 1164 helix: 2.53 (0.18), residues: 756 sheet: 0.35 (0.51), residues: 80 loop : -0.35 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 177 HIS 0.005 0.001 HIS A 125 PHE 0.017 0.002 PHE B 312 TYR 0.012 0.001 TYR B 289 ARG 0.005 0.000 ARG A 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 81 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.8990 (m-80) cc_final: 0.8481 (t80) REVERT: A 206 ARG cc_start: 0.8637 (ttp80) cc_final: 0.8103 (ttp80) REVERT: A 307 TYR cc_start: 0.8918 (OUTLIER) cc_final: 0.8708 (m-10) REVERT: A 412 ASP cc_start: 0.9079 (p0) cc_final: 0.8879 (p0) REVERT: B 157 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8562 (t80) REVERT: B 175 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8754 (tp) REVERT: B 213 MET cc_start: 0.8779 (ttt) cc_final: 0.8514 (ttt) REVERT: B 232 GLU cc_start: 0.9322 (mm-30) cc_final: 0.8914 (tp30) REVERT: B 297 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8311 (t) REVERT: B 371 ASP cc_start: 0.8771 (t0) cc_final: 0.8368 (t0) REVERT: B 466 GLU cc_start: 0.9382 (OUTLIER) cc_final: 0.9028 (mp0) outliers start: 54 outliers final: 38 residues processed: 122 average time/residue: 0.1583 time to fit residues: 29.7479 Evaluate side-chains 121 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 78 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 307 TYR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 342 HIS Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 554 HIS Chi-restraints excluded: chain B residue 568 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 91 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS B 125 HIS B 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.059692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.050710 restraints weight = 43674.054| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 5.58 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9312 Z= 0.206 Angle : 0.626 10.096 12662 Z= 0.314 Chirality : 0.039 0.167 1484 Planarity : 0.004 0.034 1602 Dihedral : 6.173 98.162 1328 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.94 % Allowed : 21.57 % Favored : 73.50 % 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: 2.57 (0.25), residues: 1164 helix: 2.63 (0.18), residues: 762 sheet: 0.39 (0.51), residues: 80 loop : -0.23 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 205 HIS 0.008 0.001 HIS B 208 PHE 0.015 0.001 PHE B 23 TYR 0.009 0.001 TYR B 289 ARG 0.007 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 81 time to evaluate : 1.046 Fit side-chains REVERT: A 157 PHE cc_start: 0.8976 (m-80) cc_final: 0.8474 (t80) REVERT: A 206 ARG cc_start: 0.8636 (ttp80) cc_final: 0.8065 (ttp80) REVERT: A 213 MET cc_start: 0.8728 (ttp) cc_final: 0.8342 (ttm) REVERT: A 320 MET cc_start: 0.9172 (ptp) cc_final: 0.8828 (pmm) REVERT: B 157 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8580 (t80) REVERT: B 175 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8729 (tp) REVERT: B 213 MET cc_start: 0.8736 (ttt) cc_final: 0.8500 (ttt) REVERT: B 232 GLU cc_start: 0.9320 (mm-30) cc_final: 0.8863 (tp30) REVERT: B 297 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8249 (t) REVERT: B 371 ASP cc_start: 0.8772 (t0) cc_final: 0.8355 (t0) REVERT: B 466 GLU cc_start: 0.9385 (OUTLIER) cc_final: 0.9001 (mt-10) outliers start: 46 outliers final: 36 residues processed: 119 average time/residue: 0.1669 time to fit residues: 30.4631 Evaluate side-chains 117 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 77 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 342 HIS Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 568 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 13 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 113 optimal weight: 0.0270 chunk 43 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 62 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS ** B 327 GLN ** 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 = 0.3256 r_free = 0.3256 target = 0.061179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.052123 restraints weight = 43072.909| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 5.54 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9312 Z= 0.179 Angle : 0.636 9.643 12662 Z= 0.311 Chirality : 0.039 0.192 1484 Planarity : 0.004 0.035 1602 Dihedral : 6.019 93.902 1328 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.97 % Allowed : 22.42 % Favored : 73.61 % 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: 2.62 (0.25), residues: 1164 helix: 2.65 (0.18), residues: 760 sheet: 0.64 (0.52), residues: 80 loop : -0.23 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 177 HIS 0.006 0.001 HIS A 125 PHE 0.013 0.001 PHE B 303 TYR 0.010 0.001 TYR A 87 ARG 0.008 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 78 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.9003 (m-80) cc_final: 0.8484 (t80) REVERT: A 206 ARG cc_start: 0.8628 (ttp80) cc_final: 0.8210 (ttp80) REVERT: A 213 MET cc_start: 0.8744 (ttp) cc_final: 0.8349 (ttm) REVERT: A 284 MET cc_start: 0.6753 (tpp) cc_final: 0.6235 (tpp) REVERT: A 320 MET cc_start: 0.9194 (ptp) cc_final: 0.8861 (pmm) REVERT: B 157 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8600 (t80) REVERT: B 175 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8689 (tp) REVERT: B 213 MET cc_start: 0.8689 (ttt) cc_final: 0.8435 (ttt) REVERT: B 232 GLU cc_start: 0.9349 (mm-30) cc_final: 0.8840 (tp30) REVERT: B 284 MET cc_start: 0.7054 (tpp) cc_final: 0.6806 (tpp) REVERT: B 297 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8231 (t) REVERT: B 371 ASP cc_start: 0.8748 (t0) cc_final: 0.8341 (t0) REVERT: B 466 GLU cc_start: 0.9384 (OUTLIER) cc_final: 0.9060 (mt-10) REVERT: B 533 GLU cc_start: 0.9464 (tt0) cc_final: 0.9008 (mt-10) outliers start: 37 outliers final: 25 residues processed: 111 average time/residue: 0.1595 time to fit residues: 26.9805 Evaluate side-chains 104 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 525 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 106 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS B 208 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.061126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.052011 restraints weight = 44001.072| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 5.61 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9312 Z= 0.184 Angle : 0.624 9.362 12662 Z= 0.306 Chirality : 0.039 0.186 1484 Planarity : 0.003 0.036 1602 Dihedral : 5.946 92.910 1328 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.33 % Allowed : 23.50 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.63 (0.25), residues: 1164 helix: 2.64 (0.18), residues: 760 sheet: 0.70 (0.52), residues: 80 loop : -0.21 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 286 HIS 0.002 0.001 HIS A 342 PHE 0.013 0.001 PHE B 23 TYR 0.008 0.001 TYR A 87 ARG 0.003 0.000 ARG B 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.9062 (m-80) cc_final: 0.8537 (t80) REVERT: A 206 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8233 (ttp80) REVERT: A 213 MET cc_start: 0.8766 (ttp) cc_final: 0.8365 (ttm) REVERT: A 284 MET cc_start: 0.6759 (tpp) cc_final: 0.6243 (tpp) REVERT: A 320 MET cc_start: 0.9222 (ptp) cc_final: 0.8902 (pmm) REVERT: B 157 PHE cc_start: 0.9023 (m-80) cc_final: 0.8624 (t80) REVERT: B 175 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8667 (tp) REVERT: B 213 MET cc_start: 0.8678 (ttt) cc_final: 0.8406 (ttt) REVERT: B 232 GLU cc_start: 0.9385 (mm-30) cc_final: 0.8657 (tp30) REVERT: B 297 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8214 (t) REVERT: B 371 ASP cc_start: 0.8763 (t0) cc_final: 0.8334 (t0) REVERT: B 466 GLU cc_start: 0.9397 (OUTLIER) cc_final: 0.9087 (mt-10) REVERT: B 533 GLU cc_start: 0.9460 (tt0) cc_final: 0.8992 (mt-10) outliers start: 31 outliers final: 26 residues processed: 105 average time/residue: 0.1891 time to fit residues: 29.6816 Evaluate side-chains 101 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 342 HIS Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 568 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 26 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 HIS B 125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.060604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.051604 restraints weight = 43011.268| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 5.50 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9312 Z= 0.212 Angle : 0.637 9.171 12662 Z= 0.313 Chirality : 0.039 0.182 1484 Planarity : 0.003 0.035 1602 Dihedral : 5.937 90.586 1328 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.65 % Allowed : 23.07 % Favored : 73.28 % 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: 2.58 (0.25), residues: 1164 helix: 2.62 (0.19), residues: 760 sheet: 0.67 (0.52), residues: 80 loop : -0.26 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 286 HIS 0.003 0.001 HIS A 125 PHE 0.013 0.001 PHE B 23 TYR 0.008 0.001 TYR A 87 ARG 0.008 0.000 ARG A 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3142.31 seconds wall clock time: 56 minutes 55.11 seconds (3415.11 seconds total)