Starting phenix.real_space_refine on Sun Jun 8 18:19:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vqt_21356/06_2025/6vqt_21356.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vqt_21356/06_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_21356/06_2025/6vqt_21356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vqt_21356/06_2025/6vqt_21356.map" model { file = "/net/cci-nas-00/data/ceres_data/6vqt_21356/06_2025/6vqt_21356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vqt_21356/06_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-5710/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: 6.13, per 1000 atoms: 0.67 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: 2.76 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.05 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: 2.86 Time building geometry restraints manager: 3.22 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: 1.840 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.460 Find NCS groups from input model: 0.470 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.320 ------------------------------------------------------------------------------- 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 : 0.011 0.426 9314 Z= 0.740 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 Details of bonding type rmsd hydrogen bonds : bond 0.16031 ( 629) hydrogen bonds : angle 5.12581 ( 1839) covalent geometry : bond 0.00899 ( 9312) covalent geometry : angle 1.15128 (12662) Misc. bond : bond 0.39717 ( 2) *********************** 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 : 1.113 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: 0.2609 time to fit residues: 55.6932 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 : 1.270 ------------------------------------------------------------------------------- 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: 3.9990 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: 1.5788 ------------------------------------------------------------------------------- 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 504 GLN B 570 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.062775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.053907 restraints weight = 42326.668| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 5.34 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9314 Z= 0.196 Angle : 0.691 10.760 12662 Z= 0.362 Chirality : 0.042 0.187 1484 Planarity : 0.005 0.052 1602 Dihedral : 7.894 112.670 1351 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.36 % Allowed : 17.60 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.24), residues: 1164 helix: 2.66 (0.17), residues: 764 sheet: 0.84 (0.53), residues: 80 loop : -0.34 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 205 HIS 0.003 0.001 HIS B 342 PHE 0.016 0.001 PHE B 58 TYR 0.009 0.001 TYR B 289 ARG 0.009 0.001 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.09476 ( 629) hydrogen bonds : angle 4.77683 ( 1839) covalent geometry : bond 0.00347 ( 9312) covalent geometry : angle 0.69127 (12662) Misc. bond : bond 0.00483 ( 2) *********************** 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 107 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 MET cc_start: 0.8800 (ttp) cc_final: 0.8500 (ttt) REVERT: A 316 ASP cc_start: 0.9343 (m-30) cc_final: 0.9120 (t0) REVERT: A 320 MET cc_start: 0.9177 (ptp) cc_final: 0.8935 (ptp) REVERT: A 371 ASP cc_start: 0.8515 (m-30) cc_final: 0.7853 (t0) REVERT: A 412 ASP cc_start: 0.9165 (p0) cc_final: 0.8955 (p0) REVERT: B 157 PHE cc_start: 0.9055 (m-80) cc_final: 0.8823 (m-80) REVERT: B 206 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7668 (ttp80) REVERT: B 213 MET cc_start: 0.8738 (ttt) cc_final: 0.8484 (ttt) REVERT: B 320 MET cc_start: 0.9281 (ptp) cc_final: 0.8973 (ptp) REVERT: B 371 ASP cc_start: 0.8244 (t0) cc_final: 0.8009 (t0) REVERT: B 419 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8850 (pp) outliers start: 22 outliers final: 16 residues processed: 104 average time/residue: 0.3141 time to fit residues: 46.2002 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 : 1.482 ------------------------------------------------------------------------------- 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: 0.0980 chunk 36 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS B 442 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.060551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.051842 restraints weight = 42877.363| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 5.27 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 9314 Z= 0.205 Angle : 0.649 10.287 12662 Z= 0.339 Chirality : 0.041 0.177 1484 Planarity : 0.004 0.044 1602 Dihedral : 7.088 103.007 1335 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.76 % Allowed : 18.13 % Favored : 78.11 % 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: 2.61 (0.24), residues: 1164 helix: 2.61 (0.18), residues: 764 sheet: 0.74 (0.53), residues: 80 loop : -0.20 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 414 HIS 0.002 0.001 HIS A 579 PHE 0.019 0.001 PHE B 58 TYR 0.010 0.001 TYR B 289 ARG 0.011 0.001 ARG A 372 Details of bonding type rmsd hydrogen bonds : bond 0.08810 ( 629) hydrogen bonds : angle 4.72317 ( 1839) covalent geometry : bond 0.00419 ( 9312) covalent geometry : angle 0.64906 (12662) Misc. bond : bond 0.00020 ( 2) *********************** 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 117 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.9083 (m-80) cc_final: 0.8641 (t80) REVERT: A 213 MET cc_start: 0.8821 (ttp) cc_final: 0.8615 (ttp) REVERT: A 412 ASP cc_start: 0.9118 (p0) cc_final: 0.8916 (p0) REVERT: B 67 MET cc_start: 0.7147 (mmt) cc_final: 0.6911 (mmt) REVERT: B 175 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8724 (tp) REVERT: B 213 MET cc_start: 0.8796 (ttt) cc_final: 0.8472 (ttt) REVERT: B 371 ASP cc_start: 0.8405 (t0) cc_final: 0.8050 (t0) REVERT: B 419 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8889 (pp) REVERT: B 466 GLU cc_start: 0.9365 (OUTLIER) cc_final: 0.8974 (mp0) outliers start: 35 outliers final: 25 residues processed: 108 average time/residue: 0.1790 time to fit residues: 28.9301 Evaluate side-chains 96 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 307 TYR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 419 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 111 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 179 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 208 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.061150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.052286 restraints weight = 42711.776| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 5.36 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9314 Z= 0.166 Angle : 0.614 10.496 12662 Z= 0.314 Chirality : 0.040 0.214 1484 Planarity : 0.004 0.041 1602 Dihedral : 6.526 98.697 1330 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.08 % Allowed : 20.28 % Favored : 75.64 % 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: 2.73 (0.24), residues: 1164 helix: 2.74 (0.18), residues: 762 sheet: 0.69 (0.52), residues: 80 loop : -0.22 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 177 HIS 0.002 0.001 HIS B 342 PHE 0.035 0.001 PHE B 312 TYR 0.010 0.001 TYR B 289 ARG 0.005 0.000 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.08141 ( 629) hydrogen bonds : angle 4.45679 ( 1839) covalent geometry : bond 0.00316 ( 9312) covalent geometry : angle 0.61434 (12662) Misc. bond : bond 0.00053 ( 2) *********************** 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 117 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 79 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.9073 (m-80) cc_final: 0.8455 (t80) REVERT: A 213 MET cc_start: 0.8781 (ttp) cc_final: 0.8580 (ttp) REVERT: A 371 ASP cc_start: 0.8668 (m-30) cc_final: 0.8171 (t70) REVERT: B 67 MET cc_start: 0.7075 (mmt) cc_final: 0.6855 (mmt) REVERT: B 157 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8513 (t80) REVERT: B 175 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8689 (tp) REVERT: B 213 MET cc_start: 0.8762 (ttt) cc_final: 0.8448 (ttt) REVERT: B 297 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8141 (t) REVERT: B 371 ASP cc_start: 0.8472 (t0) cc_final: 0.8030 (t0) REVERT: B 419 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8944 (pp) REVERT: B 466 GLU cc_start: 0.9354 (OUTLIER) cc_final: 0.8981 (mp0) outliers start: 38 outliers final: 24 residues processed: 110 average time/residue: 0.1518 time to fit residues: 26.3761 Evaluate side-chains 102 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 155 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 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 466 GLU Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 554 HIS 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: 0.5980 chunk 112 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 113 optimal weight: 0.0170 chunk 1 optimal weight: 0.7980 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN B 99 ASN B 208 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.062070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.053136 restraints weight = 42431.869| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 5.39 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9314 Z= 0.149 Angle : 0.594 10.364 12662 Z= 0.300 Chirality : 0.039 0.215 1484 Planarity : 0.003 0.039 1602 Dihedral : 6.337 99.450 1330 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.40 % Allowed : 20.17 % Favored : 75.43 % 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: 2.83 (0.24), residues: 1164 helix: 2.81 (0.18), residues: 762 sheet: 0.74 (0.52), residues: 80 loop : -0.18 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 177 HIS 0.011 0.001 HIS B 208 PHE 0.027 0.001 PHE B 312 TYR 0.009 0.001 TYR A 87 ARG 0.005 0.000 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.07651 ( 629) hydrogen bonds : angle 4.29314 ( 1839) covalent geometry : bond 0.00265 ( 9312) covalent geometry : angle 0.59353 (12662) Misc. bond : bond 0.00037 ( 2) *********************** 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 116 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 75 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.8950 (m-80) cc_final: 0.8491 (t80) REVERT: A 206 ARG cc_start: 0.8460 (ttp80) cc_final: 0.7988 (ttp80) REVERT: A 213 MET cc_start: 0.8755 (ttp) cc_final: 0.8540 (ttp) REVERT: A 284 MET cc_start: 0.7087 (tpp) cc_final: 0.6822 (tpp) REVERT: A 320 MET cc_start: 0.9152 (ptp) cc_final: 0.8753 (pmm) REVERT: A 371 ASP cc_start: 0.8667 (m-30) cc_final: 0.8156 (t70) REVERT: B 157 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8543 (t80) REVERT: B 175 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8692 (tp) REVERT: B 213 MET cc_start: 0.8748 (ttt) cc_final: 0.8442 (ttt) REVERT: B 297 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8159 (t) REVERT: B 371 ASP cc_start: 0.8515 (t0) cc_final: 0.8042 (t0) REVERT: B 466 GLU cc_start: 0.9358 (OUTLIER) cc_final: 0.8988 (mp0) outliers start: 41 outliers final: 29 residues processed: 110 average time/residue: 0.1560 time to fit residues: 26.3048 Evaluate side-chains 107 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 113 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.058546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.049949 restraints weight = 44048.131| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 5.26 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 9314 Z= 0.253 Angle : 0.678 11.076 12662 Z= 0.352 Chirality : 0.041 0.176 1484 Planarity : 0.004 0.038 1602 Dihedral : 6.418 102.968 1328 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.83 % Allowed : 20.92 % Favored : 74.25 % 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: 2.48 (0.24), residues: 1164 helix: 2.57 (0.18), residues: 762 sheet: 0.42 (0.50), residues: 80 loop : -0.34 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 177 HIS 0.005 0.001 HIS B 208 PHE 0.019 0.002 PHE B 312 TYR 0.012 0.001 TYR B 289 ARG 0.013 0.001 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.08373 ( 629) hydrogen bonds : angle 4.68691 ( 1839) covalent geometry : bond 0.00528 ( 9312) covalent geometry : angle 0.67789 (12662) Misc. bond : bond 0.00110 ( 2) *********************** 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 122 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 77 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.8985 (m-80) cc_final: 0.8513 (t80) REVERT: A 206 ARG cc_start: 0.8596 (ttp80) cc_final: 0.8071 (ttp80) REVERT: B 157 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8555 (t80) REVERT: B 175 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8783 (tp) REVERT: B 213 MET cc_start: 0.8828 (ttt) cc_final: 0.8586 (ttt) REVERT: B 232 GLU cc_start: 0.9318 (mp0) cc_final: 0.9026 (mp0) REVERT: B 297 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8277 (t) REVERT: B 371 ASP cc_start: 0.8712 (t0) cc_final: 0.8285 (t0) outliers start: 45 outliers final: 36 residues processed: 114 average time/residue: 0.1572 time to fit residues: 27.7337 Evaluate side-chains 113 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 74 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 112 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 ASN ** 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 = 0.3220 r_free = 0.3220 target = 0.060350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.051541 restraints weight = 43179.178| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 5.24 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9314 Z= 0.159 Angle : 0.620 9.973 12662 Z= 0.311 Chirality : 0.039 0.155 1484 Planarity : 0.003 0.036 1602 Dihedral : 6.179 99.088 1328 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.29 % Allowed : 22.32 % Favored : 73.39 % 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: 2.66 (0.25), residues: 1164 helix: 2.69 (0.18), residues: 762 sheet: 0.45 (0.50), residues: 80 loop : -0.19 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 177 HIS 0.002 0.000 HIS B 342 PHE 0.015 0.001 PHE B 312 TYR 0.009 0.001 TYR A 87 ARG 0.005 0.000 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.07753 ( 629) hydrogen bonds : angle 4.34107 ( 1839) covalent geometry : bond 0.00305 ( 9312) covalent geometry : angle 0.61990 (12662) Misc. bond : bond 0.00060 ( 2) *********************** 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 118 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 78 time to evaluate : 1.536 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.8993 (m-80) cc_final: 0.8503 (t80) REVERT: A 206 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8214 (ttp80) REVERT: A 320 MET cc_start: 0.9161 (ptp) cc_final: 0.8803 (pmm) REVERT: B 157 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8550 (t80) REVERT: B 175 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8709 (tp) REVERT: B 213 MET cc_start: 0.8755 (ttt) cc_final: 0.8506 (ttt) REVERT: B 297 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8258 (t) REVERT: B 371 ASP cc_start: 0.8720 (t0) cc_final: 0.8344 (t0) outliers start: 40 outliers final: 32 residues processed: 108 average time/residue: 0.1787 time to fit residues: 30.1183 Evaluate side-chains 112 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 77 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 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 307 TYR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 91 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 A 214 ASN B 208 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.061392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.052356 restraints weight = 43364.019| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 5.43 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9314 Z= 0.147 Angle : 0.626 9.516 12662 Z= 0.308 Chirality : 0.039 0.162 1484 Planarity : 0.003 0.036 1602 Dihedral : 6.033 97.276 1328 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.61 % Allowed : 22.10 % 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: 2.73 (0.25), residues: 1164 helix: 2.74 (0.18), residues: 760 sheet: 0.54 (0.51), residues: 80 loop : -0.14 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 177 HIS 0.003 0.000 HIS A 125 PHE 0.014 0.001 PHE A 312 TYR 0.009 0.001 TYR A 87 ARG 0.004 0.000 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.07205 ( 629) hydrogen bonds : angle 4.18658 ( 1839) covalent geometry : bond 0.00270 ( 9312) covalent geometry : angle 0.62552 (12662) Misc. bond : bond 0.00038 ( 2) *********************** 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 121 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 78 time to evaluate : 1.531 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.9018 (m-80) cc_final: 0.8508 (t80) REVERT: A 206 ARG cc_start: 0.8629 (ttp80) cc_final: 0.8201 (ttp80) REVERT: A 284 MET cc_start: 0.6628 (tpp) cc_final: 0.6157 (tpp) REVERT: A 320 MET cc_start: 0.9211 (ptp) cc_final: 0.8828 (pmm) REVERT: B 157 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8550 (t80) REVERT: B 175 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8677 (tp) REVERT: B 213 MET cc_start: 0.8696 (ttt) cc_final: 0.8440 (ttt) REVERT: B 284 MET cc_start: 0.7036 (tpp) cc_final: 0.6767 (tpp) REVERT: B 297 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8219 (t) REVERT: B 371 ASP cc_start: 0.8701 (t0) cc_final: 0.8306 (t0) REVERT: B 466 GLU cc_start: 0.9370 (OUTLIER) cc_final: 0.8971 (mt-10) outliers start: 43 outliers final: 33 residues processed: 114 average time/residue: 0.2890 time to fit residues: 51.3018 Evaluate side-chains 110 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 73 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 197 TRP Chi-restraints excluded: chain A residue 276 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 554 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 125 HIS 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 307 TYR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 13 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 88 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3223 r_free = 0.3223 target = 0.059762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.050995 restraints weight = 43584.577| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 5.33 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9314 Z= 0.189 Angle : 0.649 9.976 12662 Z= 0.326 Chirality : 0.039 0.165 1484 Planarity : 0.004 0.036 1602 Dihedral : 6.092 98.094 1328 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.40 % Allowed : 22.10 % 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: 2.53 (0.25), residues: 1164 helix: 2.62 (0.18), residues: 758 sheet: 0.46 (0.51), residues: 80 loop : -0.32 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 177 HIS 0.010 0.001 HIS B 208 PHE 0.012 0.001 PHE B 312 TYR 0.008 0.001 TYR B 289 ARG 0.004 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.07441 ( 629) hydrogen bonds : angle 4.38134 ( 1839) covalent geometry : bond 0.00389 ( 9312) covalent geometry : angle 0.64943 (12662) Misc. bond : bond 0.00105 ( 2) *********************** 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 120 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 79 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.8998 (m-80) cc_final: 0.8507 (t80) REVERT: A 206 ARG cc_start: 0.8690 (ttp80) cc_final: 0.8248 (ttp80) REVERT: A 213 MET cc_start: 0.8723 (ttp) cc_final: 0.8367 (ttm) REVERT: A 232 GLU cc_start: 0.8963 (tp30) cc_final: 0.8536 (tp30) REVERT: A 320 MET cc_start: 0.9192 (ptp) cc_final: 0.8829 (pmm) REVERT: B 157 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8571 (t80) REVERT: B 175 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8719 (tp) REVERT: B 208 HIS cc_start: 0.8363 (OUTLIER) cc_final: 0.8147 (t-90) REVERT: B 213 MET cc_start: 0.8722 (ttt) cc_final: 0.8471 (ttt) REVERT: B 297 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8265 (t) REVERT: B 371 ASP cc_start: 0.8742 (t0) cc_final: 0.8319 (t0) outliers start: 41 outliers final: 32 residues processed: 113 average time/residue: 0.1578 time to fit residues: 27.6675 Evaluate side-chains 114 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 78 time to evaluate : 1.219 ------------------------------------------------------------------------------- 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 197 TRP Chi-restraints excluded: chain A residue 276 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 106 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 111 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 87 optimal weight: 0.0070 chunk 36 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 overall best weight: 0.6200 ------------------------------------------------------------------------------- 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 ** 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 = 0.3274 r_free = 0.3274 target = 0.061872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.052896 restraints weight = 43112.935| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 5.46 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9314 Z= 0.146 Angle : 0.627 9.081 12662 Z= 0.308 Chirality : 0.039 0.188 1484 Planarity : 0.004 0.036 1602 Dihedral : 5.940 93.053 1328 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.65 % Allowed : 22.75 % 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: 2.69 (0.25), residues: 1164 helix: 2.68 (0.19), residues: 762 sheet: 0.65 (0.51), residues: 80 loop : -0.13 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 177 HIS 0.018 0.001 HIS A 125 PHE 0.010 0.001 PHE B 303 TYR 0.010 0.001 TYR A 87 ARG 0.004 0.000 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.06990 ( 629) hydrogen bonds : angle 4.12288 ( 1839) covalent geometry : bond 0.00263 ( 9312) covalent geometry : angle 0.62726 (12662) Misc. bond : bond 0.00019 ( 2) ********************** 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: 34 poor density : 73 time to evaluate : 1.621 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.5808 (mmt) cc_final: 0.5600 (mmt) REVERT: A 157 PHE cc_start: 0.9012 (m-80) cc_final: 0.8503 (t80) REVERT: A 206 ARG cc_start: 0.8674 (ttp80) cc_final: 0.8235 (ttp80) REVERT: A 213 MET cc_start: 0.8733 (ttp) cc_final: 0.8363 (ttm) REVERT: A 232 GLU cc_start: 0.8939 (tp30) cc_final: 0.8521 (tp30) REVERT: A 284 MET cc_start: 0.6672 (tpp) cc_final: 0.6199 (tpp) REVERT: A 320 MET cc_start: 0.9202 (ptp) cc_final: 0.8866 (pmm) REVERT: B 157 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8561 (t80) REVERT: B 175 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8683 (tp) REVERT: B 213 MET cc_start: 0.8684 (ttt) cc_final: 0.8411 (ttt) REVERT: B 284 MET cc_start: 0.6842 (tpp) cc_final: 0.6511 (tpp) REVERT: B 297 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8208 (t) REVERT: B 371 ASP cc_start: 0.8721 (t0) cc_final: 0.8300 (t0) REVERT: B 466 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.9076 (mt-10) outliers start: 34 outliers final: 28 residues processed: 103 average time/residue: 0.2103 time to fit residues: 33.2809 Evaluate side-chains 104 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 72 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL 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 197 TRP Chi-restraints excluded: chain A residue 276 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 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 511 THR Chi-restraints excluded: chain B residue 513 VAL 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 26 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 208 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.059699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.050737 restraints weight = 43335.400| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 5.44 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9314 Z= 0.199 Angle : 0.662 9.732 12662 Z= 0.332 Chirality : 0.040 0.175 1484 Planarity : 0.004 0.036 1602 Dihedral : 6.042 93.428 1328 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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: 2.51 (0.25), residues: 1164 helix: 2.59 (0.19), residues: 760 sheet: 0.47 (0.51), residues: 80 loop : -0.30 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 177 HIS 0.026 0.001 HIS A 125 PHE 0.036 0.002 PHE B 521 TYR 0.009 0.001 TYR B 289 ARG 0.003 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.07341 ( 629) hydrogen bonds : angle 4.39639 ( 1839) covalent geometry : bond 0.00414 ( 9312) covalent geometry : angle 0.66174 (12662) Misc. bond : bond 0.00103 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3575.28 seconds wall clock time: 64 minutes 17.50 seconds (3857.50 seconds total)