Starting phenix.real_space_refine on Wed Sep 25 07:31:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqt_21356/09_2024/6vqt_21356.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqt_21356/09_2024/6vqt_21356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqt_21356/09_2024/6vqt_21356.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqt_21356/09_2024/6vqt_21356.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqt_21356/09_2024/6vqt_21356.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqt_21356/09_2024/6vqt_21356.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 657 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians V 2 8.30 5 P 4 5.49 5 Mg 2 5.21 5 S 24 5.16 5 C 5822 2.51 5 N 1620 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9144 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4539 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 15, 'TRANS': 568} Chain: "B" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4539 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 15, 'TRANS': 568} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 38 Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.13, per 1000 atoms: 0.67 Number of scatterers: 9144 At special positions: 0 Unit cell: (72.437, 91.1854, 141.465, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 2 22.97 S 24 16.00 P 4 15.00 Mg 2 11.99 O 1670 8.00 N 1620 7.00 C 5822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 981.2 milliseconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2164 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 4 sheets defined 72.1% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 15 through 28 Proline residue: A 25 - end of helix removed outlier: 3.662A pdb=" N TRP A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 68 removed outlier: 3.511A pdb=" N ARG A 36 " --> pdb=" O ASN A 32 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Proline residue: A 57 - end of helix removed outlier: 3.542A pdb=" N THR A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 127 removed outlier: 5.040A pdb=" N ARG A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL A 108 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 109 " --> pdb=" O PHE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 removed outlier: 4.219A pdb=" N ALA A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 161 removed outlier: 3.593A pdb=" N VAL A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 180 Processing helix chain 'A' and resid 182 through 230 removed outlier: 4.335A pdb=" N HIS A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU A 209 " --> pdb=" O TRP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 239 through 293 removed outlier: 3.846A pdb=" N ALA A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 319 Proline residue: A 314 - end of helix removed outlier: 3.762A pdb=" N LEU A 318 " --> pdb=" O PRO A 314 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 341 removed outlier: 3.535A pdb=" N THR A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 408 removed outlier: 3.895A pdb=" N ALA A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 450 through 457 Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 499 through 515 Processing helix chain 'A' and resid 529 through 544 Processing helix chain 'A' and resid 555 through 560 removed outlier: 3.591A pdb=" N ALA A 560 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 587 through 598 Processing helix chain 'B' and resid 16 through 28 Proline residue: B 25 - end of helix removed outlier: 3.550A pdb=" N TRP B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 68 Proline residue: B 57 - end of helix removed outlier: 3.507A pdb=" N MET B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 127 removed outlier: 3.503A pdb=" N VAL B 95 " --> pdb=" O ARG B 91 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ARG B 107 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N VAL B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY B 109 " --> pdb=" O PHE B 105 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 removed outlier: 4.151A pdb=" N HIS B 132 " --> pdb=" O SER B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 161 removed outlier: 3.741A pdb=" N VAL B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 180 Processing helix chain 'B' and resid 182 through 230 removed outlier: 4.103A pdb=" N HIS B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU B 209 " --> pdb=" O TRP B 205 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 212 " --> pdb=" O HIS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 239 through 293 removed outlier: 3.771A pdb=" N ALA B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 319 removed outlier: 3.962A pdb=" N VAL B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) Proline residue: B 314 - end of helix removed outlier: 3.703A pdb=" N MET B 317 " --> pdb=" O ARG B 313 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU B 318 " --> pdb=" O PRO B 314 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 341 removed outlier: 3.572A pdb=" N THR B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 408 removed outlier: 4.365A pdb=" N ALA B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 428 No H-bonds generated for 'chain 'B' and resid 426 through 428' Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 450 through 457 Processing helix chain 'B' and resid 463 through 474 Processing helix chain 'B' and resid 476 through 482 Processing helix chain 'B' and resid 485 through 489 Processing helix chain 'B' and resid 499 through 515 Processing helix chain 'B' and resid 529 through 544 Processing helix chain 'B' and resid 555 through 560 removed outlier: 3.586A pdb=" N ALA B 560 " --> pdb=" O SER B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 586 Processing helix chain 'B' and resid 587 through 598 Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 384 removed outlier: 7.217A pdb=" N HIS A 378 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL A 367 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU A 380 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN A 365 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL A 366 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLU A 415 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 437 through 440 removed outlier: 6.563A pdb=" N LEU A 519 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE A 552 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE A 521 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 390 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG A 389 " --> pdb=" O THR A 564 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LEU A 566 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA A 391 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU A 568 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 393 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE A 565 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLN A 576 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL A 567 " --> pdb=" O ALA A 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 377 through 384 removed outlier: 7.449A pdb=" N HIS B 378 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL B 367 " --> pdb=" O HIS B 378 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU B 380 " --> pdb=" O ASN B 365 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN B 365 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL B 366 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLU B 415 " --> pdb=" O VAL B 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 437 through 440 removed outlier: 6.676A pdb=" N GLY B 438 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASP B 522 " --> pdb=" O GLY B 438 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B 440 " --> pdb=" O ASP B 522 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 519 " --> pdb=" O ILE B 550 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE B 552 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE B 521 " --> pdb=" O ILE B 552 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL B 390 " --> pdb=" O SER B 551 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ARG B 389 " --> pdb=" O THR B 564 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU B 566 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ALA B 391 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU B 568 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL B 393 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ILE B 565 " --> pdb=" O GLN B 576 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLN B 576 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL B 567 " --> pdb=" O ALA B 574 " (cutoff:3.500A) 629 hydrogen bonds defined for protein. 1839 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3021 1.34 - 1.46: 1165 1.46 - 1.57: 5062 1.57 - 1.69: 8 1.69 - 1.80: 56 Bond restraints: 9312 Sorted by residual: bond pdb=" C1' ADP B 701 " pdb=" C2' ADP B 701 " ideal model delta sigma weight residual 1.524 1.293 0.231 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C1' ADP A 701 " pdb=" C2' ADP A 701 " ideal model delta sigma weight residual 1.524 1.293 0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C1' ADP A 701 " pdb=" O4' ADP A 701 " ideal model delta sigma weight residual 1.426 1.624 -0.198 2.00e-02 2.50e+03 9.77e+01 bond pdb=" C1' ADP B 701 " pdb=" O4' ADP B 701 " ideal model delta sigma weight residual 1.426 1.623 -0.197 2.00e-02 2.50e+03 9.69e+01 bond pdb=" C4 ADP B 701 " pdb=" C5 ADP B 701 " ideal model delta sigma weight residual 1.490 1.335 0.155 2.00e-02 2.50e+03 6.01e+01 ... (remaining 9307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 12457 3.36 - 6.72: 168 6.72 - 10.08: 15 10.08 - 13.44: 8 13.44 - 16.79: 14 Bond angle restraints: 12662 Sorted by residual: angle pdb=" N VAL B 321 " pdb=" CA VAL B 321 " pdb=" C VAL B 321 " ideal model delta sigma weight residual 113.20 105.73 7.47 9.60e-01 1.09e+00 6.05e+01 angle pdb=" O2 VO4 A 702 " pdb=" V VO4 A 702 " pdb=" O4 VO4 A 702 " ideal model delta sigma weight residual 109.47 126.26 -16.79 3.00e+00 1.11e-01 3.13e+01 angle pdb=" O3 VO4 A 702 " pdb=" V VO4 A 702 " pdb=" O4 VO4 A 702 " ideal model delta sigma weight residual 109.47 126.16 -16.68 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O3 VO4 A 704 " pdb=" V VO4 A 704 " pdb=" O4 VO4 A 704 " ideal model delta sigma weight residual 109.47 126.07 -16.59 3.00e+00 1.11e-01 3.06e+01 angle pdb=" O2 VO4 A 704 " pdb=" V VO4 A 704 " pdb=" O4 VO4 A 704 " ideal model delta sigma weight residual 109.47 125.57 -16.10 3.00e+00 1.11e-01 2.88e+01 ... (remaining 12657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.78: 5270 30.78 - 61.57: 216 61.57 - 92.35: 21 92.35 - 123.14: 1 123.14 - 153.92: 2 Dihedral angle restraints: 5510 sinusoidal: 2144 harmonic: 3366 Sorted by residual: dihedral pdb=" C5' ADP B 701 " pdb=" O5' ADP B 701 " pdb=" PA ADP B 701 " pdb=" O2A ADP B 701 " ideal model delta sinusoidal sigma weight residual -60.00 93.92 -153.92 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" O1B ADP B 701 " pdb=" O3A ADP B 701 " pdb=" PB ADP B 701 " pdb=" PA ADP B 701 " ideal model delta sinusoidal sigma weight residual 300.00 170.92 129.07 1 2.00e+01 2.50e-03 3.91e+01 dihedral pdb=" C5' ADP A 701 " pdb=" O5' ADP A 701 " pdb=" PA ADP A 701 " pdb=" O2A ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 62.49 -122.49 1 2.00e+01 2.50e-03 3.69e+01 ... (remaining 5507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.187: 1480 0.187 - 0.375: 2 0.375 - 0.562: 0 0.562 - 0.749: 0 0.749 - 0.936: 2 Chirality restraints: 1484 Sorted by residual: chirality pdb=" V VO4 A 704 " pdb=" O1 VO4 A 704 " pdb=" O2 VO4 A 704 " pdb=" O4 VO4 A 704 " both_signs ideal model delta sigma weight residual True 5.36 -4.43 0.94 2.00e-01 2.50e+01 2.19e+01 chirality pdb=" V VO4 A 702 " pdb=" O1 VO4 A 702 " pdb=" O2 VO4 A 702 " pdb=" O4 VO4 A 702 " both_signs ideal model delta sigma weight residual True 5.36 4.44 0.92 2.00e-01 2.50e+01 2.14e+01 chirality pdb=" CG LEU B 582 " pdb=" CB LEU B 582 " pdb=" CD1 LEU B 582 " pdb=" CD2 LEU B 582 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1481 not shown) Planarity restraints: 1602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 74 " 0.053 5.00e-02 4.00e+02 7.98e-02 1.02e+01 pdb=" N PRO B 75 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 75 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 75 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 401 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.53e+00 pdb=" C SER A 401 " -0.051 2.00e-02 2.50e+03 pdb=" O SER A 401 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 402 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 313 " 0.044 5.00e-02 4.00e+02 6.61e-02 7.00e+00 pdb=" N PRO B 314 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 314 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 314 " 0.037 5.00e-02 4.00e+02 ... (remaining 1599 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 23 2.37 - 3.00: 5304 3.00 - 3.63: 13339 3.63 - 4.27: 18479 4.27 - 4.90: 30362 Nonbonded interactions: 67507 Sorted by model distance: nonbonded pdb=" V VO4 A 704 " pdb="MG MG B 702 " model vdw 1.733 2.180 nonbonded pdb=" O2B ADP B 701 " pdb="MG MG B 702 " model vdw 1.891 2.170 nonbonded pdb=" O4 VO4 A 704 " pdb="MG MG B 702 " model vdw 1.895 2.170 nonbonded pdb=" O3B ADP A 701 " pdb="MG MG A 703 " model vdw 1.920 2.170 nonbonded pdb=" O2 VO4 A 704 " pdb="MG MG B 702 " model vdw 1.969 2.170 ... (remaining 67502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 598 or resid 701)) selection = (chain 'B' and (resid 15 through 598 or resid 701)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.280 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.231 9312 Z= 0.620 Angle : 1.151 16.795 12662 Z= 0.653 Chirality : 0.061 0.936 1484 Planarity : 0.006 0.080 1602 Dihedral : 16.315 153.919 3346 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.94 % Allowed : 13.41 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.23), residues: 1164 helix: 1.65 (0.16), residues: 760 sheet: 0.63 (0.54), residues: 78 loop : -0.68 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 177 HIS 0.005 0.002 HIS A 115 PHE 0.020 0.002 PHE B 58 TYR 0.025 0.002 TYR B 289 ARG 0.013 0.002 ARG A 434 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 115 time to evaluate : 1.015 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: 0.2478 time to fit residues: 52.2886 Evaluate side-chains 98 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 443 ASP Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 205 TRP Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 342 HIS Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 525 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 32 ASN A 208 HIS A 263 ASN A 293 GLN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN A 570 GLN B 18 GLN B 74 GLN B 161 ASN B 293 GLN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN B 442 GLN B 504 GLN B 570 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9312 Z= 0.219 Angle : 0.683 10.101 12662 Z= 0.357 Chirality : 0.042 0.180 1484 Planarity : 0.005 0.064 1602 Dihedral : 7.771 108.443 1351 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.47 % Allowed : 18.03 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.24), residues: 1164 helix: 2.70 (0.17), residues: 764 sheet: 0.84 (0.53), residues: 80 loop : -0.32 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 205 HIS 0.004 0.001 HIS B 208 PHE 0.017 0.001 PHE B 58 TYR 0.009 0.001 TYR A 87 ARG 0.006 0.001 ARG B 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: A 213 MET cc_start: 0.8401 (ttp) cc_final: 0.8168 (ttt) REVERT: B 206 ARG cc_start: 0.7543 (ttp80) cc_final: 0.7266 (ttp80) outliers start: 23 outliers final: 16 residues processed: 108 average time/residue: 0.2227 time to fit residues: 33.6831 Evaluate side-chains 94 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 342 HIS Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 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 58 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 114 optimal weight: 0.9980 chunk 93 optimal weight: 0.0170 chunk 104 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9312 Z= 0.184 Angle : 0.629 10.542 12662 Z= 0.321 Chirality : 0.040 0.181 1484 Planarity : 0.004 0.045 1602 Dihedral : 6.781 105.702 1333 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.00 % Allowed : 19.10 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.24), residues: 1164 helix: 2.74 (0.18), residues: 764 sheet: 0.92 (0.55), residues: 80 loop : -0.16 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 177 HIS 0.003 0.000 HIS B 342 PHE 0.031 0.001 PHE B 312 TYR 0.010 0.001 TYR A 87 ARG 0.007 0.000 ARG B 313 *********************** 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 116 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 88 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 146 ARG cc_start: 0.8535 (mmm-85) cc_final: 0.8307 (tpp80) REVERT: A 157 PHE cc_start: 0.8012 (m-80) cc_final: 0.7688 (t80) REVERT: A 284 MET cc_start: 0.7021 (tpp) cc_final: 0.6792 (tpp) REVERT: B 157 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7730 (t80) REVERT: B 213 MET cc_start: 0.8422 (ttt) cc_final: 0.8177 (ttm) outliers start: 28 outliers final: 18 residues processed: 109 average time/residue: 0.2136 time to fit residues: 32.7931 Evaluate side-chains 92 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 73 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 157 PHE Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 554 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 112 optimal weight: 0.0970 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A 179 ASN A 277 ASN B 208 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9312 Z= 0.313 Angle : 0.670 9.744 12662 Z= 0.351 Chirality : 0.041 0.192 1484 Planarity : 0.004 0.040 1602 Dihedral : 6.559 103.465 1328 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 5.15 % Allowed : 19.64 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.25), residues: 1164 helix: 2.57 (0.18), residues: 760 sheet: 0.68 (0.53), residues: 80 loop : -0.28 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 177 HIS 0.003 0.001 HIS A 579 PHE 0.032 0.002 PHE B 312 TYR 0.010 0.001 TYR B 289 ARG 0.007 0.001 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 76 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.8048 (m-80) cc_final: 0.7809 (t80) REVERT: A 213 MET cc_start: 0.8453 (ttp) cc_final: 0.8214 (ttm) REVERT: B 67 MET cc_start: 0.6870 (mmt) cc_final: 0.6477 (mmt) REVERT: B 157 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7801 (t80) REVERT: B 175 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8943 (tp) outliers start: 48 outliers final: 31 residues processed: 112 average time/residue: 0.1566 time to fit residues: 27.2017 Evaluate side-chains 103 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 70 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 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 513 VAL Chi-restraints excluded: chain A residue 554 HIS 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 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 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 93 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 100 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 99 ASN B 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9312 Z= 0.204 Angle : 0.622 10.177 12662 Z= 0.316 Chirality : 0.040 0.226 1484 Planarity : 0.004 0.037 1602 Dihedral : 6.351 100.049 1328 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.65 % Allowed : 21.57 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.25), residues: 1164 helix: 2.68 (0.18), residues: 760 sheet: 0.74 (0.53), residues: 80 loop : -0.22 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 177 HIS 0.010 0.001 HIS B 208 PHE 0.037 0.001 PHE B 312 TYR 0.008 0.001 TYR B 236 ARG 0.004 0.000 ARG A 313 *********************** 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 118 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 84 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.8011 (m-80) cc_final: 0.7786 (t80) REVERT: A 284 MET cc_start: 0.7139 (tpp) cc_final: 0.6911 (tpp) REVERT: B 67 MET cc_start: 0.6831 (mmt) cc_final: 0.6374 (mmt) REVERT: B 151 ILE cc_start: 0.8905 (pt) cc_final: 0.8696 (mm) REVERT: B 157 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7762 (t80) REVERT: B 175 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8894 (tp) outliers start: 34 outliers final: 30 residues processed: 111 average time/residue: 0.1557 time to fit residues: 27.5079 Evaluate side-chains 109 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 77 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 276 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain B residue 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 298 VAL Chi-restraints excluded: chain B residue 307 TYR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 554 HIS Chi-restraints excluded: chain B residue 568 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 93 optimal weight: 0.2980 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 108 optimal weight: 0.5980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9312 Z= 0.221 Angle : 0.621 10.211 12662 Z= 0.314 Chirality : 0.039 0.202 1484 Planarity : 0.004 0.035 1602 Dihedral : 6.241 102.018 1328 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.40 % Allowed : 20.82 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.25), residues: 1164 helix: 2.66 (0.18), residues: 762 sheet: 0.74 (0.53), residues: 80 loop : -0.23 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 177 HIS 0.003 0.001 HIS B 208 PHE 0.028 0.001 PHE B 312 TYR 0.008 0.001 TYR A 87 ARG 0.004 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 78 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.8054 (m-80) cc_final: 0.7812 (t80) REVERT: A 213 MET cc_start: 0.8387 (ttp) cc_final: 0.8079 (ttm) REVERT: A 284 MET cc_start: 0.6854 (tpp) cc_final: 0.6391 (tpp) REVERT: B 67 MET cc_start: 0.6834 (mmt) cc_final: 0.6470 (mmt) REVERT: B 157 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7842 (t80) REVERT: B 175 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8886 (tp) outliers start: 41 outliers final: 32 residues processed: 110 average time/residue: 0.1461 time to fit residues: 25.3637 Evaluate side-chains 110 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 76 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 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 513 VAL Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 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 551 SER Chi-restraints excluded: chain B residue 554 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 504 GLN B 208 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9312 Z= 0.262 Angle : 0.644 10.124 12662 Z= 0.328 Chirality : 0.040 0.162 1484 Planarity : 0.004 0.034 1602 Dihedral : 6.262 102.747 1328 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.26 % Allowed : 20.17 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.25), residues: 1164 helix: 2.56 (0.18), residues: 760 sheet: 0.49 (0.52), residues: 80 loop : -0.29 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 177 HIS 0.005 0.001 HIS A 125 PHE 0.025 0.002 PHE B 312 TYR 0.010 0.001 TYR B 289 ARG 0.004 0.000 ARG A 101 *********************** 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 127 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 78 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.8083 (m-80) cc_final: 0.7836 (t80) REVERT: B 67 MET cc_start: 0.6989 (mmt) cc_final: 0.6644 (mmt) REVERT: B 157 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7881 (t80) REVERT: B 175 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8888 (tp) outliers start: 49 outliers final: 40 residues processed: 117 average time/residue: 0.1771 time to fit residues: 32.1357 Evaluate side-chains 118 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 76 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 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 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 46 VAL Chi-restraints excluded: chain B residue 101 ARG 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 511 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 551 SER Chi-restraints excluded: chain B residue 554 HIS Chi-restraints excluded: chain B residue 568 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9312 Z= 0.203 Angle : 0.635 9.772 12662 Z= 0.317 Chirality : 0.039 0.156 1484 Planarity : 0.004 0.034 1602 Dihedral : 6.154 100.172 1328 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.94 % Allowed : 20.60 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.25), residues: 1164 helix: 2.63 (0.18), residues: 762 sheet: 0.51 (0.52), residues: 80 loop : -0.21 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 286 HIS 0.005 0.001 HIS A 125 PHE 0.020 0.001 PHE B 312 TYR 0.008 0.001 TYR A 87 ARG 0.003 0.000 ARG A 313 *********************** 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 124 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 78 time to evaluate : 1.021 Fit side-chains REVERT: A 157 PHE cc_start: 0.8065 (m-80) cc_final: 0.7816 (t80) REVERT: A 213 MET cc_start: 0.8382 (ttp) cc_final: 0.8096 (ttm) REVERT: A 284 MET cc_start: 0.6820 (tpp) cc_final: 0.6465 (tpp) REVERT: B 67 MET cc_start: 0.6960 (mmt) cc_final: 0.6621 (mmt) REVERT: B 101 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7990 (ptt90) REVERT: B 157 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7894 (t80) REVERT: B 175 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8867 (tp) outliers start: 46 outliers final: 36 residues processed: 114 average time/residue: 0.1669 time to fit residues: 29.2236 Evaluate side-chains 117 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 78 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 554 HIS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 101 ARG 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 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 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 107 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9312 Z= 0.275 Angle : 0.665 10.066 12662 Z= 0.333 Chirality : 0.040 0.186 1484 Planarity : 0.004 0.036 1602 Dihedral : 6.200 99.858 1328 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.40 % Allowed : 21.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.25), residues: 1164 helix: 2.57 (0.18), residues: 760 sheet: 0.45 (0.51), residues: 80 loop : -0.36 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 177 HIS 0.005 0.001 HIS A 125 PHE 0.020 0.001 PHE B 312 TYR 0.010 0.001 TYR B 289 ARG 0.004 0.000 ARG A 101 *********************** 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 119 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 78 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.8110 (m-80) cc_final: 0.7851 (t80) REVERT: A 213 MET cc_start: 0.8424 (ttp) cc_final: 0.8131 (ttm) REVERT: A 284 MET cc_start: 0.6866 (tpp) cc_final: 0.6519 (tpp) REVERT: B 67 MET cc_start: 0.7016 (mmt) cc_final: 0.6642 (mmt) REVERT: B 101 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8020 (ptt90) REVERT: B 157 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7955 (t80) REVERT: B 175 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8880 (tp) REVERT: B 213 MET cc_start: 0.8425 (tpp) cc_final: 0.8213 (tpp) outliers start: 41 outliers final: 34 residues processed: 109 average time/residue: 0.1578 time to fit residues: 26.6144 Evaluate side-chains 113 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 76 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 342 HIS Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 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 46 VAL Chi-restraints excluded: chain B residue 101 ARG Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 305 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 106 optimal weight: 0.0980 chunk 92 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 98 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9312 Z= 0.194 Angle : 0.647 10.059 12662 Z= 0.318 Chirality : 0.039 0.187 1484 Planarity : 0.004 0.034 1602 Dihedral : 6.085 96.055 1328 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.76 % Allowed : 22.00 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.25), residues: 1164 helix: 2.63 (0.18), residues: 762 sheet: 0.59 (0.52), residues: 80 loop : -0.26 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 286 HIS 0.012 0.001 HIS B 125 PHE 0.017 0.001 PHE B 312 TYR 0.009 0.001 TYR A 87 ARG 0.004 0.000 ARG B 123 ********************** 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 111 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 76 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 157 PHE cc_start: 0.8075 (m-80) cc_final: 0.7821 (t80) REVERT: A 213 MET cc_start: 0.8391 (ttp) cc_final: 0.8092 (ttm) REVERT: A 284 MET cc_start: 0.6804 (tpp) cc_final: 0.6477 (tpp) REVERT: B 67 MET cc_start: 0.6979 (mmt) cc_final: 0.6658 (mmt) REVERT: B 157 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7920 (t80) REVERT: B 175 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8843 (tp) REVERT: B 213 MET cc_start: 0.8411 (tpp) cc_final: 0.8202 (tpp) REVERT: B 284 MET cc_start: 0.7134 (tpp) cc_final: 0.6873 (tpp) outliers start: 35 outliers final: 30 residues processed: 106 average time/residue: 0.1639 time to fit residues: 26.2159 Evaluate side-chains 107 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 75 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 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 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 513 VAL Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 554 HIS 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 298 VAL Chi-restraints excluded: chain B residue 342 HIS Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 358 ARG Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 568 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.059197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.050289 restraints weight = 43663.933| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 5.49 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9312 Z= 0.266 Angle : 0.667 9.661 12662 Z= 0.334 Chirality : 0.040 0.163 1484 Planarity : 0.004 0.035 1602 Dihedral : 6.189 95.203 1328 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.97 % Allowed : 21.46 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.25), residues: 1164 helix: 2.55 (0.18), residues: 760 sheet: 0.53 (0.52), residues: 80 loop : -0.39 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 177 HIS 0.011 0.001 HIS B 208 PHE 0.036 0.002 PHE A 312 TYR 0.009 0.001 TYR B 289 ARG 0.006 0.000 ARG B 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1816.68 seconds wall clock time: 33 minutes 9.49 seconds (1989.49 seconds total)