Starting phenix.real_space_refine on Wed Sep 17 16:44:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vqt_21356/09_2025/6vqt_21356.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vqt_21356/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6vqt_21356/09_2025/6vqt_21356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vqt_21356/09_2025/6vqt_21356.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vqt_21356/09_2025/6vqt_21356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vqt_21356/09_2025/6vqt_21356.map" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.23, per 1000 atoms: 0.24 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: 0.85 Conformation dependent library (CDL) restraints added in 283.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.29 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: 1.52 Time building geometry restraints manager: 1.04 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 701) selection = (chain 'B' and resid 15 through 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.660 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.090 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.013 0.002 ARG A 434 TYR 0.025 0.002 TYR B 289 PHE 0.020 0.002 PHE B 58 TRP 0.029 0.002 TRP A 177 HIS 0.005 0.002 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00899 ( 9312) covalent geometry : angle 1.15128 (12662) hydrogen bonds : bond 0.16031 ( 629) hydrogen bonds : angle 5.12581 ( 1839) 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 : 0.306 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: 0.1116 time to fit residues: 23.5687 Evaluate side-chains 98 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 108 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 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 18 GLN A 32 ASN A 208 HIS A 263 ASN A 293 GLN ** A 327 GLN ** 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 423 GLN B 442 GLN B 504 GLN B 570 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.061352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.052628 restraints weight = 43122.562| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 5.32 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9314 Z= 0.216 Angle : 0.706 10.305 12662 Z= 0.372 Chirality : 0.042 0.174 1484 Planarity : 0.005 0.062 1602 Dihedral : 7.862 107.651 1351 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.90 % Allowed : 17.81 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.58 (0.24), residues: 1164 helix: 2.62 (0.17), residues: 764 sheet: 0.79 (0.52), residues: 80 loop : -0.32 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 313 TYR 0.010 0.001 TYR B 457 PHE 0.021 0.002 PHE B 58 TRP 0.019 0.001 TRP B 177 HIS 0.004 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9312) covalent geometry : angle 0.70562 (12662) hydrogen bonds : bond 0.09541 ( 629) hydrogen bonds : angle 4.91228 ( 1839) Misc. bond : bond 0.00113 ( 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 113 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ARG cc_start: 0.7880 (ttp80) cc_final: 0.7635 (ttp80) REVERT: A 213 MET cc_start: 0.8848 (ttp) cc_final: 0.8543 (ttt) REVERT: A 316 ASP cc_start: 0.9379 (m-30) cc_final: 0.9138 (t0) REVERT: A 412 ASP cc_start: 0.9134 (p0) cc_final: 0.8933 (p0) REVERT: B 157 PHE cc_start: 0.9055 (m-80) cc_final: 0.8848 (m-80) REVERT: B 206 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7674 (ttp80) REVERT: B 213 MET cc_start: 0.8792 (ttt) cc_final: 0.8581 (ttt) REVERT: B 320 MET cc_start: 0.9280 (ptp) cc_final: 0.8995 (ptp) REVERT: B 371 ASP cc_start: 0.8272 (t0) cc_final: 0.8048 (t0) REVERT: B 419 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8902 (pp) outliers start: 27 outliers final: 20 residues processed: 107 average time/residue: 0.0988 time to fit residues: 14.7184 Evaluate side-chains 97 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 270 ILE Chi-restraints excluded: chain A residue 288 VAL 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 513 VAL Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 155 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 25 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 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 = 0.3228 r_free = 0.3228 target = 0.061075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.052330 restraints weight = 43261.393| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 5.37 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2523 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= 0.178 Angle : 0.623 10.036 12662 Z= 0.323 Chirality : 0.040 0.158 1484 Planarity : 0.004 0.045 1602 Dihedral : 6.963 103.979 1335 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.18 % Allowed : 18.13 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.67 (0.24), residues: 1164 helix: 2.66 (0.18), residues: 764 sheet: 0.74 (0.53), residues: 80 loop : -0.19 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 372 TYR 0.011 0.001 TYR B 289 PHE 0.020 0.001 PHE B 312 TRP 0.015 0.001 TRP B 177 HIS 0.002 0.001 HIS B 342 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9312) covalent geometry : angle 0.62275 (12662) hydrogen bonds : bond 0.08518 ( 629) hydrogen bonds : angle 4.59369 ( 1839) 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: 39 poor density : 78 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 146 ARG cc_start: 0.9047 (mmm-85) cc_final: 0.8837 (tpp80) REVERT: A 157 PHE cc_start: 0.9148 (m-80) cc_final: 0.8559 (t80) REVERT: A 213 MET cc_start: 0.8793 (ttp) cc_final: 0.8563 (ttp) REVERT: A 284 MET cc_start: 0.7249 (tpp) cc_final: 0.7041 (tpp) REVERT: A 371 ASP cc_start: 0.8625 (m-30) cc_final: 0.8081 (t70) REVERT: B 67 MET cc_start: 0.7141 (mmt) cc_final: 0.6914 (mmt) REVERT: B 175 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8720 (tp) REVERT: B 213 MET cc_start: 0.8780 (ttt) cc_final: 0.8465 (ttt) REVERT: B 297 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.8075 (t) REVERT: B 371 ASP cc_start: 0.8406 (t0) cc_final: 0.8052 (t0) REVERT: B 419 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8930 (pp) REVERT: B 466 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.8992 (mp0) outliers start: 39 outliers final: 27 residues processed: 109 average time/residue: 0.0747 time to fit residues: 12.3520 Evaluate side-chains 99 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 68 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 270 ILE 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 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 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 551 SER Chi-restraints excluded: chain B residue 554 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 0.0870 chunk 54 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 277 ASN A 504 GLN B 208 HIS B 214 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.057951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.049424 restraints weight = 44953.859| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 5.31 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 9314 Z= 0.236 Angle : 0.669 10.612 12662 Z= 0.351 Chirality : 0.041 0.147 1484 Planarity : 0.004 0.041 1602 Dihedral : 6.695 102.622 1330 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.26 % Allowed : 20.82 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.24), residues: 1164 helix: 2.52 (0.18), residues: 758 sheet: 0.49 (0.51), residues: 80 loop : -0.35 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 313 TYR 0.013 0.001 TYR B 289 PHE 0.022 0.002 PHE B 58 TRP 0.019 0.001 TRP B 177 HIS 0.003 0.001 HIS A 579 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 9312) covalent geometry : angle 0.66856 (12662) hydrogen bonds : bond 0.08971 ( 629) hydrogen bonds : angle 4.77313 ( 1839) Misc. bond : bond 0.00082 ( 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 125 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 76 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.9114 (m-80) cc_final: 0.8468 (t80) REVERT: A 371 ASP cc_start: 0.8786 (m-30) cc_final: 0.8226 (t70) REVERT: B 157 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8566 (t80) REVERT: B 175 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8761 (tp) REVERT: B 213 MET cc_start: 0.8819 (ttt) cc_final: 0.8538 (ttt) REVERT: B 371 ASP cc_start: 0.8596 (t0) cc_final: 0.8136 (t0) REVERT: B 419 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8998 (pp) outliers start: 49 outliers final: 35 residues processed: 114 average time/residue: 0.0691 time to fit residues: 12.2485 Evaluate side-chains 109 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 71 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 270 ILE 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 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 46 VAL 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 288 VAL 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 355 VAL Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 419 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 214 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** 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 = 0.3195 r_free = 0.3195 target = 0.059389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.050640 restraints weight = 43516.607| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 5.32 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3178 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= 0.168 Angle : 0.610 10.450 12662 Z= 0.312 Chirality : 0.039 0.147 1484 Planarity : 0.004 0.039 1602 Dihedral : 6.499 100.694 1330 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.83 % Allowed : 21.14 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.62 (0.24), residues: 1164 helix: 2.66 (0.18), residues: 764 sheet: 0.52 (0.51), residues: 80 loop : -0.27 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 146 TYR 0.009 0.001 TYR B 289 PHE 0.019 0.001 PHE B 312 TRP 0.009 0.001 TRP B 177 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9312) covalent geometry : angle 0.60958 (12662) hydrogen bonds : bond 0.08364 ( 629) hydrogen bonds : angle 4.47517 ( 1839) Misc. bond : bond 0.00059 ( 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 123 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 78 time to evaluate : 0.352 Fit side-chains REVERT: A 157 PHE cc_start: 0.8944 (m-80) cc_final: 0.8434 (t80) REVERT: A 213 MET cc_start: 0.8708 (ttp) cc_final: 0.8221 (ttm) REVERT: A 284 MET cc_start: 0.7172 (tpp) cc_final: 0.6900 (tpp) REVERT: A 320 MET cc_start: 0.9162 (ptp) cc_final: 0.8751 (pmm) REVERT: A 371 ASP cc_start: 0.8760 (m-30) cc_final: 0.8239 (t70) REVERT: B 157 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8572 (t80) REVERT: B 175 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8743 (tp) REVERT: B 213 MET cc_start: 0.8785 (ttt) cc_final: 0.8515 (ttt) REVERT: B 297 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8262 (t) REVERT: B 371 ASP cc_start: 0.8670 (t0) cc_final: 0.8237 (t0) REVERT: B 466 GLU cc_start: 0.9340 (OUTLIER) cc_final: 0.8997 (mp0) outliers start: 45 outliers final: 35 residues processed: 113 average time/residue: 0.0676 time to fit residues: 12.0612 Evaluate side-chains 115 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 76 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 270 ILE Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 305 ASN 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 513 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 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 466 GLU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 554 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 64 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 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 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 = 0.3178 r_free = 0.3178 target = 0.058721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.050040 restraints weight = 44272.071| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 5.35 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3376 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= 0.203 Angle : 0.642 10.812 12662 Z= 0.328 Chirality : 0.040 0.149 1484 Planarity : 0.004 0.036 1602 Dihedral : 6.379 102.356 1328 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.04 % Allowed : 21.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.24), residues: 1164 helix: 2.55 (0.18), residues: 764 sheet: 0.40 (0.50), residues: 80 loop : -0.27 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 313 TYR 0.011 0.001 TYR B 289 PHE 0.028 0.001 PHE B 312 TRP 0.012 0.001 TRP B 177 HIS 0.002 0.001 HIS A 579 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 9312) covalent geometry : angle 0.64173 (12662) hydrogen bonds : bond 0.08281 ( 629) hydrogen bonds : angle 4.56790 ( 1839) Misc. bond : bond 0.00096 ( 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 127 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 80 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.8958 (m-80) cc_final: 0.8476 (t80) REVERT: A 206 ARG cc_start: 0.8696 (ttp80) cc_final: 0.7945 (ttp80) REVERT: A 213 MET cc_start: 0.8728 (ttp) cc_final: 0.8249 (ttm) REVERT: A 284 MET cc_start: 0.7191 (tpp) cc_final: 0.6913 (tpp) REVERT: B 157 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8570 (t80) REVERT: B 175 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8750 (tp) REVERT: B 213 MET cc_start: 0.8803 (ttt) cc_final: 0.8546 (ttt) REVERT: B 297 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8285 (t) REVERT: B 371 ASP cc_start: 0.8755 (t0) cc_final: 0.8314 (t0) outliers start: 47 outliers final: 38 residues processed: 116 average time/residue: 0.0735 time to fit residues: 12.9126 Evaluate side-chains 117 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 76 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 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 155 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 305 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 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 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 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 91 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 ** 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 = 0.3191 r_free = 0.3191 target = 0.058701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.049868 restraints weight = 43971.728| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 5.44 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9314 Z= 0.184 Angle : 0.642 10.477 12662 Z= 0.323 Chirality : 0.039 0.148 1484 Planarity : 0.004 0.036 1602 Dihedral : 6.282 100.410 1328 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 5.26 % Allowed : 21.57 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.25), residues: 1164 helix: 2.57 (0.18), residues: 762 sheet: 0.35 (0.50), residues: 80 loop : -0.30 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 313 TYR 0.010 0.001 TYR B 289 PHE 0.023 0.001 PHE B 312 TRP 0.011 0.001 TRP B 177 HIS 0.002 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9312) covalent geometry : angle 0.64170 (12662) hydrogen bonds : bond 0.08080 ( 629) hydrogen bonds : angle 4.48075 ( 1839) Misc. bond : bond 0.00094 ( 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 129 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 80 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.8996 (m-80) cc_final: 0.8501 (t80) REVERT: A 206 ARG cc_start: 0.8744 (ttp80) cc_final: 0.7952 (ttp80) REVERT: A 284 MET cc_start: 0.7145 (tpp) cc_final: 0.6861 (tpp) REVERT: A 317 MET cc_start: 0.9371 (tmm) cc_final: 0.9142 (tmm) REVERT: A 320 MET cc_start: 0.9256 (ptp) cc_final: 0.8843 (pmm) REVERT: B 157 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8599 (t80) REVERT: B 175 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8712 (tp) REVERT: B 213 MET cc_start: 0.8750 (ttt) cc_final: 0.8492 (ttt) REVERT: B 297 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8265 (t) REVERT: B 371 ASP cc_start: 0.8786 (t0) cc_final: 0.8387 (t0) REVERT: B 466 GLU cc_start: 0.9376 (OUTLIER) cc_final: 0.9029 (mp0) REVERT: B 533 GLU cc_start: 0.9456 (tt0) cc_final: 0.8980 (mt-10) outliers start: 49 outliers final: 38 residues processed: 120 average time/residue: 0.0589 time to fit residues: 11.2596 Evaluate side-chains 118 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 76 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL 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 143 VAL Chi-restraints excluded: chain A residue 155 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 305 ASN Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 554 HIS Chi-restraints excluded: chain B residue 568 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 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 = 0.3178 r_free = 0.3178 target = 0.058228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.049476 restraints weight = 43876.098| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 5.39 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9314 Z= 0.212 Angle : 0.670 10.621 12662 Z= 0.339 Chirality : 0.040 0.158 1484 Planarity : 0.004 0.035 1602 Dihedral : 6.316 98.861 1328 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.90 % Allowed : 22.00 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.25), residues: 1164 helix: 2.53 (0.18), residues: 760 sheet: 0.31 (0.51), residues: 80 loop : -0.35 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 123 TYR 0.011 0.001 TYR B 289 PHE 0.023 0.002 PHE B 312 TRP 0.012 0.001 TRP B 177 HIS 0.007 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9312) covalent geometry : angle 0.67010 (12662) hydrogen bonds : bond 0.08149 ( 629) hydrogen bonds : angle 4.58835 ( 1839) Misc. bond : bond 0.00125 ( 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 132 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 77 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.8984 (m-80) cc_final: 0.8477 (t80) REVERT: A 206 ARG cc_start: 0.8791 (ttp80) cc_final: 0.8014 (ttp80) REVERT: A 232 GLU cc_start: 0.9326 (OUTLIER) cc_final: 0.9057 (mp0) REVERT: A 284 MET cc_start: 0.6966 (tpp) cc_final: 0.6634 (tpp) REVERT: A 317 MET cc_start: 0.9382 (tmm) cc_final: 0.9142 (tmm) REVERT: A 320 MET cc_start: 0.9248 (ptp) cc_final: 0.8849 (pmm) REVERT: B 157 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8588 (t80) REVERT: B 175 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8721 (tp) REVERT: B 213 MET cc_start: 0.8781 (ttt) cc_final: 0.8534 (ttt) REVERT: B 297 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8274 (t) REVERT: B 371 ASP cc_start: 0.8832 (t0) cc_final: 0.8410 (t0) outliers start: 55 outliers final: 42 residues processed: 119 average time/residue: 0.0640 time to fit residues: 12.1237 Evaluate side-chains 122 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 76 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL 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 143 VAL Chi-restraints excluded: chain A residue 155 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 232 GLU Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 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 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 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 554 HIS Chi-restraints excluded: chain B residue 568 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 94 optimal weight: 0.0050 chunk 41 optimal weight: 0.0870 chunk 113 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 93 optimal weight: 0.0770 chunk 13 optimal weight: 2.9990 overall best weight: 0.3730 ------------------------------------------------------------------------------- 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 = 0.3247 r_free = 0.3247 target = 0.060717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.051668 restraints weight = 43081.310| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 5.51 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9314 Z= 0.160 Angle : 0.652 9.573 12662 Z= 0.322 Chirality : 0.040 0.202 1484 Planarity : 0.004 0.036 1602 Dihedral : 6.072 92.147 1328 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.86 % Allowed : 23.93 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.59 (0.25), residues: 1164 helix: 2.63 (0.18), residues: 762 sheet: 0.56 (0.52), residues: 80 loop : -0.24 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 123 TYR 0.010 0.001 TYR A 87 PHE 0.016 0.001 PHE B 312 TRP 0.016 0.001 TRP A 177 HIS 0.005 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9312) covalent geometry : angle 0.65179 (12662) hydrogen bonds : bond 0.07428 ( 629) hydrogen bonds : angle 4.19563 ( 1839) Misc. bond : bond 0.00022 ( 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 111 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 75 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.8964 (m-80) cc_final: 0.8507 (t80) REVERT: A 206 ARG cc_start: 0.8768 (ttp80) cc_final: 0.7968 (ttp80) REVERT: A 284 MET cc_start: 0.6795 (tpp) cc_final: 0.6295 (tpp) REVERT: A 317 MET cc_start: 0.9346 (tmm) cc_final: 0.9036 (tmm) REVERT: A 320 MET cc_start: 0.9255 (ptp) cc_final: 0.8869 (pmm) REVERT: B 157 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8623 (t80) REVERT: B 175 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8657 (tp) REVERT: B 213 MET cc_start: 0.8660 (ttt) cc_final: 0.8404 (ttt) REVERT: B 284 MET cc_start: 0.7032 (tpp) cc_final: 0.6767 (tpp) REVERT: B 297 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8223 (t) REVERT: B 320 MET cc_start: 0.9587 (ptp) cc_final: 0.9246 (pmm) REVERT: B 371 ASP cc_start: 0.8797 (t0) cc_final: 0.8347 (t70) REVERT: B 466 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.9045 (mt-10) outliers start: 36 outliers final: 25 residues processed: 106 average time/residue: 0.0684 time to fit residues: 11.2852 Evaluate side-chains 101 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 197 TRP 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 355 VAL Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 525 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 68 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 105 optimal weight: 0.0370 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 overall best weight: 1.3864 ------------------------------------------------------------------------------- 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 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS B 208 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.060102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.051050 restraints weight = 43669.513| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 5.55 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9314 Z= 0.153 Angle : 0.638 9.313 12662 Z= 0.314 Chirality : 0.040 0.181 1484 Planarity : 0.003 0.035 1602 Dihedral : 6.018 92.147 1328 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.97 % Allowed : 24.14 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.25), residues: 1164 helix: 2.65 (0.18), residues: 762 sheet: 0.62 (0.52), residues: 80 loop : -0.26 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 313 TYR 0.009 0.001 TYR A 307 PHE 0.017 0.001 PHE B 312 TRP 0.016 0.001 TRP B 286 HIS 0.006 0.001 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9312) covalent geometry : angle 0.63834 (12662) hydrogen bonds : bond 0.07170 ( 629) hydrogen bonds : angle 4.23824 ( 1839) Misc. bond : bond 0.00049 ( 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 109 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 67 MET cc_start: 0.5669 (OUTLIER) cc_final: 0.5466 (mmt) REVERT: A 157 PHE cc_start: 0.8990 (m-80) cc_final: 0.8555 (t80) REVERT: A 206 ARG cc_start: 0.8764 (ttp80) cc_final: 0.7967 (ttp80) REVERT: A 213 MET cc_start: 0.8738 (ttp) cc_final: 0.8331 (ttm) REVERT: A 284 MET cc_start: 0.6723 (tpp) cc_final: 0.6224 (tpp) REVERT: A 317 MET cc_start: 0.9359 (tmm) cc_final: 0.9050 (tmm) REVERT: A 320 MET cc_start: 0.9268 (ptp) cc_final: 0.8887 (pmm) REVERT: B 157 PHE cc_start: 0.9028 (m-80) cc_final: 0.8629 (t80) REVERT: B 175 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8651 (tp) REVERT: B 213 MET cc_start: 0.8684 (ttt) cc_final: 0.8408 (ttt) REVERT: B 297 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8243 (t) REVERT: B 320 MET cc_start: 0.9590 (ptp) cc_final: 0.9254 (pmm) REVERT: B 371 ASP cc_start: 0.8811 (t0) cc_final: 0.8357 (t70) REVERT: B 466 GLU cc_start: 0.9388 (OUTLIER) cc_final: 0.9087 (mt-10) REVERT: B 533 GLU cc_start: 0.9465 (tt0) cc_final: 0.8997 (mt-10) outliers start: 37 outliers final: 26 residues processed: 104 average time/residue: 0.0663 time to fit residues: 10.7673 Evaluate side-chains 103 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 73 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 197 TRP 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 355 VAL Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 525 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 38 optimal weight: 0.4980 chunk 108 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 105 optimal weight: 0.0370 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.9064 ------------------------------------------------------------------------------- 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 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.060017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.051050 restraints weight = 43041.731| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 5.47 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3990 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= 0.163 Angle : 0.649 9.354 12662 Z= 0.320 Chirality : 0.040 0.190 1484 Planarity : 0.004 0.035 1602 Dihedral : 5.999 87.667 1328 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.54 % Allowed : 24.57 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.25), residues: 1164 helix: 2.59 (0.19), residues: 762 sheet: 0.56 (0.52), residues: 80 loop : -0.32 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 101 TYR 0.008 0.001 TYR A 87 PHE 0.032 0.001 PHE A 312 TRP 0.011 0.001 TRP A 286 HIS 0.002 0.001 HIS B 125 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9312) covalent geometry : angle 0.64863 (12662) hydrogen bonds : bond 0.07240 ( 629) hydrogen bonds : angle 4.28465 ( 1839) Misc. bond : bond 0.00053 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1469.32 seconds wall clock time: 26 minutes 3.09 seconds (1563.09 seconds total)