Starting phenix.real_space_refine on Tue Nov 18 22:18:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l2v_23142/11_2025/7l2v_23142.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l2v_23142/11_2025/7l2v_23142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l2v_23142/11_2025/7l2v_23142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l2v_23142/11_2025/7l2v_23142.map" model { file = "/net/cci-nas-00/data/ceres_data/7l2v_23142/11_2025/7l2v_23142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l2v_23142/11_2025/7l2v_23142.cif" } resolution = 3.64 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 100 5.16 5 Na 1 4.78 5 C 11543 2.51 5 N 2813 2.21 5 O 3137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17594 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "D" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "B" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "C" Number of atoms: 4349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4349 Classifications: {'peptide': 536} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 521} Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' NA': 1, '6EU': 1, 'XPS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.98, per 1000 atoms: 0.23 Number of scatterers: 17594 At special positions: 0 Unit cell: (126.92, 126.92, 111.055, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 Na 1 11.00 O 3137 8.00 N 2813 7.00 C 11543 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 716.8 milliseconds 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4056 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 4 sheets defined 64.6% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 203 through 211 Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.647A pdb=" N LYS A 237 " --> pdb=" O ASP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 324 through 328 removed outlier: 3.562A pdb=" N GLU A 327 " --> pdb=" O LYS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 345 through 354 removed outlier: 3.752A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 410 through 414 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.575A pdb=" N PHE A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 Processing helix chain 'A' and resid 468 through 500 Processing helix chain 'A' and resid 510 through 532 Processing helix chain 'A' and resid 536 through 551 Processing helix chain 'A' and resid 552 through 557 Processing helix chain 'A' and resid 562 through 599 removed outlier: 3.918A pdb=" N ALA A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 642 Processing helix chain 'A' and resid 655 through 672 removed outlier: 3.535A pdb=" N ILE A 672 " --> pdb=" O ILE A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 691 removed outlier: 3.823A pdb=" N ASN A 676 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 712 removed outlier: 3.910A pdb=" N LYS A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 211 Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.593A pdb=" N LYS D 237 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 286 through 294 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 324 through 328 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 354 Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 410 through 414 Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.534A pdb=" N PHE D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 454 Processing helix chain 'D' and resid 468 through 500 Processing helix chain 'D' and resid 510 through 532 Processing helix chain 'D' and resid 536 through 551 Processing helix chain 'D' and resid 552 through 557 Processing helix chain 'D' and resid 562 through 599 removed outlier: 4.030A pdb=" N ALA D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 642 Processing helix chain 'D' and resid 655 through 672 Processing helix chain 'D' and resid 673 through 691 removed outlier: 3.661A pdb=" N ILE D 689 " --> pdb=" O THR D 685 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 711 removed outlier: 4.088A pdb=" N LYS D 698 " --> pdb=" O LYS D 694 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 699 " --> pdb=" O ASN D 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 211 Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 270 Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 410 through 414 Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.529A pdb=" N PHE B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 454 Processing helix chain 'B' and resid 468 through 500 Processing helix chain 'B' and resid 510 through 532 Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.529A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 Processing helix chain 'B' and resid 562 through 599 removed outlier: 4.397A pdb=" N ALA B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 567 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 642 Processing helix chain 'B' and resid 655 through 671 Processing helix chain 'B' and resid 672 through 690 removed outlier: 3.724A pdb=" N ASN B 676 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 689 " --> pdb=" O THR B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 711 removed outlier: 3.911A pdb=" N LYS B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 211 Processing helix chain 'C' and resid 213 through 223 Processing helix chain 'C' and resid 233 through 237 removed outlier: 3.660A pdb=" N LYS C 237 " --> pdb=" O ASP C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 270 Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 324 through 328 Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.852A pdb=" N GLN C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 410 through 414 removed outlier: 3.567A pdb=" N LEU C 413 " --> pdb=" O HIS C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.615A pdb=" N PHE C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 454 Processing helix chain 'C' and resid 468 through 500 Processing helix chain 'C' and resid 510 through 532 Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.533A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 557 Processing helix chain 'C' and resid 562 through 575 removed outlier: 4.215A pdb=" N ALA C 566 " --> pdb=" O MET C 562 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 567 " --> pdb=" O GLY C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 599 removed outlier: 3.513A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 642 Processing helix chain 'C' and resid 655 through 672 Processing helix chain 'C' and resid 673 through 689 removed outlier: 3.632A pdb=" N ILE C 689 " --> pdb=" O THR C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 711 Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 373 removed outlier: 6.735A pdb=" N SER A 379 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA A 373 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 368 through 373 removed outlier: 6.655A pdb=" N SER D 379 " --> pdb=" O GLU D 371 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA D 373 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 368 through 373 removed outlier: 6.634A pdb=" N SER B 379 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ALA B 373 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 368 through 373 removed outlier: 6.720A pdb=" N SER C 379 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA C 373 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) 1010 hydrogen bonds defined for protein. 2907 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: 2.84 Time building geometry restraints manager: 2.05 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: 5074 1.34 - 1.46: 3623 1.46 - 1.58: 9171 1.58 - 1.70: 0 1.70 - 1.81: 164 Bond restraints: 18032 Sorted by residual: bond pdb=" CBK 6EU D 901 " pdb=" OAF 6EU D 901 " ideal model delta sigma weight residual 1.329 1.454 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" CBK 6EU A 901 " pdb=" OAF 6EU A 901 " ideal model delta sigma weight residual 1.329 1.452 -0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" CBK 6EU B 901 " pdb=" OAF 6EU B 901 " ideal model delta sigma weight residual 1.329 1.452 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" CBK 6EU C 901 " pdb=" OAF 6EU C 901 " ideal model delta sigma weight residual 1.329 1.450 -0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" C GLU A 249 " pdb=" N LEU A 250 " ideal model delta sigma weight residual 1.331 1.372 -0.040 1.59e-02 3.96e+03 6.46e+00 ... (remaining 18027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 23633 2.00 - 3.99: 680 3.99 - 5.99: 126 5.99 - 7.99: 17 7.99 - 9.99: 7 Bond angle restraints: 24463 Sorted by residual: angle pdb=" C CYS A 390 " pdb=" N GLU A 391 " pdb=" CA GLU A 391 " ideal model delta sigma weight residual 121.54 128.55 -7.01 1.91e+00 2.74e-01 1.35e+01 angle pdb=" C CYS B 390 " pdb=" N GLU B 391 " pdb=" CA GLU B 391 " ideal model delta sigma weight residual 121.54 128.44 -6.90 1.91e+00 2.74e-01 1.31e+01 angle pdb=" C CYS C 390 " pdb=" N GLU C 391 " pdb=" CA GLU C 391 " ideal model delta sigma weight residual 121.54 128.10 -6.56 1.91e+00 2.74e-01 1.18e+01 angle pdb=" CBM 6EU A 901 " pdb=" CBK 6EU A 901 " pdb=" OAF 6EU A 901 " ideal model delta sigma weight residual 110.82 120.81 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" N PHE B 712 " pdb=" CA PHE B 712 " pdb=" C PHE B 712 " ideal model delta sigma weight residual 110.80 117.87 -7.07 2.13e+00 2.20e-01 1.10e+01 ... (remaining 24458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 10145 16.06 - 32.12: 606 32.12 - 48.18: 88 48.18 - 64.24: 29 64.24 - 80.30: 17 Dihedral angle restraints: 10885 sinusoidal: 4565 harmonic: 6320 Sorted by residual: dihedral pdb=" CA VAL C 415 " pdb=" C VAL C 415 " pdb=" N GLU C 416 " pdb=" CA GLU C 416 " ideal model delta harmonic sigma weight residual -180.00 -153.76 -26.24 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA VAL B 415 " pdb=" C VAL B 415 " pdb=" N GLU B 416 " pdb=" CA GLU B 416 " ideal model delta harmonic sigma weight residual -180.00 -154.65 -25.35 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA PHE D 712 " pdb=" C PHE D 712 " pdb=" N LEU D 713 " pdb=" CA LEU D 713 " ideal model delta harmonic sigma weight residual 180.00 155.54 24.46 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 10882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2640 0.090 - 0.180: 107 0.180 - 0.269: 1 0.269 - 0.359: 0 0.359 - 0.449: 4 Chirality restraints: 2752 Sorted by residual: chirality pdb=" CAO 6EU B 901 " pdb=" CAJ 6EU B 901 " pdb=" CAR 6EU B 901 " pdb=" CAW 6EU B 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.68 0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CAO 6EU D 901 " pdb=" CAJ 6EU D 901 " pdb=" CAR 6EU D 901 " pdb=" CAW 6EU D 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.67 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CAO 6EU A 901 " pdb=" CAJ 6EU A 901 " pdb=" CAR 6EU A 901 " pdb=" CAW 6EU A 901 " both_signs ideal model delta sigma weight residual False -2.24 -2.66 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 2749 not shown) Planarity restraints: 3012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 541 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C MET A 541 " -0.047 2.00e-02 2.50e+03 pdb=" O MET A 541 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 542 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 700 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.37e+00 pdb=" C GLN D 700 " -0.047 2.00e-02 2.50e+03 pdb=" O GLN D 700 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG D 701 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 539 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.18e+00 pdb=" C ALA B 539 " 0.046 2.00e-02 2.50e+03 pdb=" O ALA B 539 " -0.017 2.00e-02 2.50e+03 pdb=" N SER B 540 " -0.016 2.00e-02 2.50e+03 ... (remaining 3009 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 173 2.63 - 3.19: 16271 3.19 - 3.76: 26613 3.76 - 4.33: 36484 4.33 - 4.90: 60705 Nonbonded interactions: 140246 Sorted by model distance: nonbonded pdb=" O1 XPS B 902 " pdb=" O4 XPS B 902 " model vdw 2.056 3.040 nonbonded pdb=" OG1 THR D 731 " pdb=" OD1 ASP D 733 " model vdw 2.126 3.040 nonbonded pdb=" OG1 THR A 731 " pdb=" OD1 ASP A 733 " model vdw 2.203 3.040 nonbonded pdb=" NH2 ARG A 557 " pdb=" OE1 GLU A 570 " model vdw 2.229 3.120 nonbonded pdb=" OG1 THR C 731 " pdb=" OD1 ASP C 733 " model vdw 2.229 3.040 ... (remaining 140241 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' selection = (chain 'B' and resid 193 through 901) selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.990 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 : 0.010 0.881 18033 Z= 0.738 Angle : 0.850 9.985 24463 Z= 0.449 Chirality : 0.046 0.449 2752 Planarity : 0.005 0.034 3012 Dihedral : 11.254 80.300 6829 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.37 % Allowed : 0.79 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 0.76 (0.17), residues: 2136 helix: 1.58 (0.14), residues: 1260 sheet: -0.70 (0.46), residues: 84 loop : -1.13 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 721 TYR 0.017 0.002 TYR A 738 PHE 0.042 0.002 PHE C 304 TRP 0.017 0.002 TRP D 372 HIS 0.006 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00731 (18032) covalent geometry : angle 0.84993 (24463) hydrogen bonds : bond 0.14123 ( 1010) hydrogen bonds : angle 5.03387 ( 2907) Misc. bond : bond 0.88149 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 729 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 TYR cc_start: 0.6752 (m-80) cc_final: 0.5854 (m-80) REVERT: A 378 HIS cc_start: 0.7887 (p-80) cc_final: 0.6588 (p-80) REVERT: A 504 LYS cc_start: 0.8996 (mttt) cc_final: 0.8522 (mmmt) REVERT: A 536 GLU cc_start: 0.8797 (mp0) cc_final: 0.8464 (mp0) REVERT: A 688 LYS cc_start: 0.9008 (tttt) cc_final: 0.8500 (tppt) REVERT: D 250 LEU cc_start: 0.8592 (mt) cc_final: 0.8389 (mp) REVERT: D 253 SER cc_start: 0.9468 (m) cc_final: 0.8819 (p) REVERT: D 326 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8562 (mt-10) REVERT: D 383 ASP cc_start: 0.7942 (p0) cc_final: 0.7514 (t0) REVERT: D 406 THR cc_start: 0.8436 (m) cc_final: 0.8123 (p) REVERT: D 410 HIS cc_start: 0.8264 (m-70) cc_final: 0.7569 (m-70) REVERT: D 506 LEU cc_start: 0.9414 (tp) cc_final: 0.9202 (tp) REVERT: D 510 SER cc_start: 0.9152 (m) cc_final: 0.8858 (p) REVERT: D 511 TYR cc_start: 0.9088 (t80) cc_final: 0.8716 (t80) REVERT: D 562 MET cc_start: 0.8760 (mmm) cc_final: 0.8257 (mmp) REVERT: D 688 LYS cc_start: 0.8890 (tptt) cc_final: 0.8651 (tptt) REVERT: D 697 TRP cc_start: 0.8430 (t60) cc_final: 0.7843 (t60) REVERT: D 738 TYR cc_start: 0.8102 (m-80) cc_final: 0.7841 (m-80) REVERT: B 222 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8533 (mm-30) REVERT: B 315 LEU cc_start: 0.9553 (mt) cc_final: 0.9339 (mp) REVERT: B 326 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8588 (mt-10) REVERT: B 368 LYS cc_start: 0.8024 (tttt) cc_final: 0.7512 (tttt) REVERT: B 378 HIS cc_start: 0.8192 (p-80) cc_final: 0.7955 (p-80) REVERT: B 397 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8297 (mt-10) REVERT: B 423 GLN cc_start: 0.8546 (tp40) cc_final: 0.8207 (tp-100) REVERT: B 656 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8594 (tptm) REVERT: C 202 GLN cc_start: 0.8073 (tt0) cc_final: 0.7704 (tm-30) REVERT: C 203 THR cc_start: 0.8140 (t) cc_final: 0.7539 (p) REVERT: C 228 GLN cc_start: 0.8432 (mt0) cc_final: 0.8087 (pm20) REVERT: C 308 MET cc_start: 0.9168 (mmm) cc_final: 0.8884 (mmm) REVERT: C 309 TYR cc_start: 0.9186 (t80) cc_final: 0.8941 (t80) REVERT: C 324 LYS cc_start: 0.8878 (mttt) cc_final: 0.8511 (mttm) REVERT: C 359 GLU cc_start: 0.8287 (tt0) cc_final: 0.7971 (tt0) REVERT: C 378 HIS cc_start: 0.8234 (p-80) cc_final: 0.6583 (p90) REVERT: C 397 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8135 (mt-10) REVERT: C 406 THR cc_start: 0.8420 (m) cc_final: 0.8066 (p) REVERT: C 423 GLN cc_start: 0.8568 (tp40) cc_final: 0.8266 (tp-100) REVERT: C 481 SER cc_start: 0.9600 (m) cc_final: 0.9132 (p) REVERT: C 506 LEU cc_start: 0.9545 (tp) cc_final: 0.9291 (tp) REVERT: C 510 SER cc_start: 0.8705 (m) cc_final: 0.8250 (p) REVERT: C 511 TYR cc_start: 0.9062 (t80) cc_final: 0.8833 (t80) REVERT: C 562 MET cc_start: 0.8854 (mmm) cc_final: 0.8481 (mmp) REVERT: C 592 SER cc_start: 0.9321 (t) cc_final: 0.9084 (p) outliers start: 7 outliers final: 0 residues processed: 734 average time/residue: 0.1445 time to fit residues: 156.5343 Evaluate side-chains 488 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 487 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 656 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 223 ASN D 494 GLN B 378 HIS C 223 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.128039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.097942 restraints weight = 38036.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.101062 restraints weight = 18229.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.103115 restraints weight = 11644.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.104412 restraints weight = 8826.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.104885 restraints weight = 7433.199| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18033 Z= 0.146 Angle : 0.619 6.596 24463 Z= 0.327 Chirality : 0.040 0.189 2752 Planarity : 0.004 0.041 3012 Dihedral : 5.902 59.708 2761 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.95 % Allowed : 10.71 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 1.39 (0.18), residues: 2136 helix: 2.15 (0.14), residues: 1284 sheet: -0.28 (0.48), residues: 76 loop : -1.13 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 432 TYR 0.015 0.001 TYR C 584 PHE 0.027 0.002 PHE D 580 TRP 0.019 0.001 TRP B 372 HIS 0.002 0.001 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00314 (18032) covalent geometry : angle 0.61858 (24463) hydrogen bonds : bond 0.05147 ( 1010) hydrogen bonds : angle 3.96304 ( 2907) Misc. bond : bond 0.00706 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 555 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 MET cc_start: 0.8955 (mmm) cc_final: 0.8375 (mtp) REVERT: A 374 TYR cc_start: 0.6630 (m-80) cc_final: 0.5576 (m-80) REVERT: A 504 LYS cc_start: 0.8886 (mttt) cc_final: 0.8494 (mmmt) REVERT: A 536 GLU cc_start: 0.8529 (mp0) cc_final: 0.8152 (mp0) REVERT: A 648 GLU cc_start: 0.8465 (tt0) cc_final: 0.8026 (pp20) REVERT: D 250 LEU cc_start: 0.8560 (mt) cc_final: 0.8332 (mt) REVERT: D 253 SER cc_start: 0.9306 (m) cc_final: 0.8809 (p) REVERT: D 308 MET cc_start: 0.9141 (mmm) cc_final: 0.8666 (mmm) REVERT: D 332 LYS cc_start: 0.9456 (mmmm) cc_final: 0.9219 (mtmm) REVERT: D 369 PHE cc_start: 0.6765 (t80) cc_final: 0.6471 (t80) REVERT: D 383 ASP cc_start: 0.8054 (p0) cc_final: 0.7525 (t0) REVERT: D 406 THR cc_start: 0.8402 (m) cc_final: 0.8113 (p) REVERT: D 552 MET cc_start: 0.8885 (tpp) cc_final: 0.8685 (tpp) REVERT: B 202 GLN cc_start: 0.8532 (tt0) cc_final: 0.8113 (tt0) REVERT: B 211 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8757 (mmm-85) REVERT: B 228 GLN cc_start: 0.7946 (mp10) cc_final: 0.7709 (mp10) REVERT: B 293 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7681 (mt-10) REVERT: B 378 HIS cc_start: 0.8190 (p90) cc_final: 0.7247 (p-80) REVERT: B 397 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8067 (mt-10) REVERT: B 423 GLN cc_start: 0.8616 (tp40) cc_final: 0.8395 (tp-100) REVERT: B 513 GLU cc_start: 0.8292 (mp0) cc_final: 0.7912 (mt-10) REVERT: B 656 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8661 (tttm) REVERT: B 700 GLN cc_start: 0.8948 (tp40) cc_final: 0.8587 (tp40) REVERT: C 203 THR cc_start: 0.8136 (t) cc_final: 0.7219 (p) REVERT: C 219 LEU cc_start: 0.9559 (tp) cc_final: 0.9245 (tp) REVERT: C 222 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8546 (mt-10) REVERT: C 228 GLN cc_start: 0.8446 (mt0) cc_final: 0.8158 (pm20) REVERT: C 309 TYR cc_start: 0.9135 (t80) cc_final: 0.8900 (t80) REVERT: C 378 HIS cc_start: 0.7765 (p-80) cc_final: 0.7388 (p90) REVERT: C 403 SER cc_start: 0.8574 (p) cc_final: 0.8104 (m) REVERT: C 423 GLN cc_start: 0.8682 (tp40) cc_final: 0.8477 (tp-100) REVERT: C 481 SER cc_start: 0.9587 (m) cc_final: 0.9188 (p) REVERT: C 562 MET cc_start: 0.8941 (mmm) cc_final: 0.8426 (mmp) REVERT: C 700 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8567 (tp-100) REVERT: C 746 GLU cc_start: 0.7745 (pt0) cc_final: 0.7278 (pt0) outliers start: 37 outliers final: 19 residues processed: 569 average time/residue: 0.1323 time to fit residues: 114.7390 Evaluate side-chains 514 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 493 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 550 THR Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 656 LYS Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 703 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 166 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 159 optimal weight: 20.0000 chunk 178 optimal weight: 4.9990 chunk 185 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 206 optimal weight: 0.0030 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 GLN D 700 GLN B 202 GLN B 393 ASN ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.127525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.096107 restraints weight = 39276.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.099151 restraints weight = 18843.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.101158 restraints weight = 12177.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.102424 restraints weight = 9322.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.103236 restraints weight = 7907.030| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18033 Z= 0.131 Angle : 0.584 10.919 24463 Z= 0.305 Chirality : 0.039 0.279 2752 Planarity : 0.004 0.054 3012 Dihedral : 5.324 54.305 2761 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.01 % Allowed : 12.97 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 1.49 (0.18), residues: 2136 helix: 2.25 (0.14), residues: 1284 sheet: -0.10 (0.50), residues: 76 loop : -1.12 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 701 TYR 0.016 0.001 TYR A 666 PHE 0.023 0.001 PHE B 304 TRP 0.013 0.001 TRP B 740 HIS 0.005 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00279 (18032) covalent geometry : angle 0.58444 (24463) hydrogen bonds : bond 0.04564 ( 1010) hydrogen bonds : angle 3.81406 ( 2907) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 521 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLN cc_start: 0.7920 (tt0) cc_final: 0.7225 (tm-30) REVERT: A 304 PHE cc_start: 0.7704 (t80) cc_final: 0.6632 (t80) REVERT: A 308 MET cc_start: 0.9127 (mmm) cc_final: 0.8468 (mtp) REVERT: A 374 TYR cc_start: 0.6758 (m-80) cc_final: 0.6048 (m-80) REVERT: A 481 SER cc_start: 0.9620 (m) cc_final: 0.9167 (p) REVERT: A 504 LYS cc_start: 0.8936 (mttt) cc_final: 0.8495 (mmmt) REVERT: A 562 MET cc_start: 0.8796 (mmm) cc_final: 0.8193 (mmm) REVERT: A 648 GLU cc_start: 0.8537 (tt0) cc_final: 0.8019 (pp20) REVERT: D 211 ARG cc_start: 0.9323 (mmt180) cc_final: 0.9057 (mpt90) REVERT: D 253 SER cc_start: 0.9272 (m) cc_final: 0.8875 (p) REVERT: D 308 MET cc_start: 0.9257 (mmm) cc_final: 0.9008 (mmm) REVERT: D 369 PHE cc_start: 0.6836 (t80) cc_final: 0.6494 (t80) REVERT: D 383 ASP cc_start: 0.8098 (p0) cc_final: 0.7416 (t0) REVERT: D 406 THR cc_start: 0.8471 (m) cc_final: 0.8170 (p) REVERT: D 716 MET cc_start: 0.5799 (ttm) cc_final: 0.5239 (tpt) REVERT: B 228 GLN cc_start: 0.7918 (mp10) cc_final: 0.7679 (mp10) REVERT: B 293 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7656 (mt-10) REVERT: B 397 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8178 (mt-10) REVERT: B 423 GLN cc_start: 0.8667 (tp40) cc_final: 0.8417 (tp-100) REVERT: B 491 ARG cc_start: 0.9037 (mmm-85) cc_final: 0.8765 (mmm-85) REVERT: B 513 GLU cc_start: 0.8354 (mp0) cc_final: 0.7894 (mt-10) REVERT: B 656 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8610 (tttp) REVERT: B 700 GLN cc_start: 0.9018 (tp40) cc_final: 0.8727 (tp40) REVERT: C 213 ASN cc_start: 0.8764 (t0) cc_final: 0.8526 (t0) REVERT: C 219 LEU cc_start: 0.9508 (tp) cc_final: 0.9207 (tp) REVERT: C 222 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8487 (mt-10) REVERT: C 228 GLN cc_start: 0.8431 (mt0) cc_final: 0.8165 (pm20) REVERT: C 294 VAL cc_start: 0.9381 (t) cc_final: 0.9130 (m) REVERT: C 308 MET cc_start: 0.9212 (mmm) cc_final: 0.8814 (mtp) REVERT: C 309 TYR cc_start: 0.9212 (t80) cc_final: 0.8884 (t80) REVERT: C 383 ASP cc_start: 0.8132 (t0) cc_final: 0.7843 (t0) REVERT: C 481 SER cc_start: 0.9610 (m) cc_final: 0.9215 (p) REVERT: C 562 MET cc_start: 0.8943 (mmm) cc_final: 0.8405 (mmp) REVERT: C 700 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8794 (mm-40) outliers start: 57 outliers final: 33 residues processed: 544 average time/residue: 0.1263 time to fit residues: 106.2493 Evaluate side-chains 518 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 484 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 727 GLN Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 550 THR Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 656 LYS Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 677 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 127 optimal weight: 0.0980 chunk 47 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 198 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 57 optimal weight: 0.1980 chunk 101 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 727 GLN D 228 GLN ** C 202 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 = 0.3667 r_free = 0.3667 target = 0.128671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.097340 restraints weight = 38952.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.100452 restraints weight = 18647.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.102513 restraints weight = 11958.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.103769 restraints weight = 9097.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104370 restraints weight = 7726.205| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18033 Z= 0.119 Angle : 0.583 11.910 24463 Z= 0.300 Chirality : 0.038 0.188 2752 Planarity : 0.003 0.041 3012 Dihedral : 4.920 53.903 2761 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.53 % Allowed : 15.98 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 1.59 (0.19), residues: 2136 helix: 2.32 (0.14), residues: 1280 sheet: 0.21 (0.54), residues: 76 loop : -1.09 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 701 TYR 0.021 0.001 TYR A 666 PHE 0.021 0.001 PHE A 266 TRP 0.015 0.001 TRP D 372 HIS 0.006 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00256 (18032) covalent geometry : angle 0.58272 (24463) hydrogen bonds : bond 0.04141 ( 1010) hydrogen bonds : angle 3.74226 ( 2907) Misc. bond : bond 0.00039 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 518 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLN cc_start: 0.7772 (tt0) cc_final: 0.7320 (tm-30) REVERT: A 304 PHE cc_start: 0.7733 (t80) cc_final: 0.6962 (t80) REVERT: A 308 MET cc_start: 0.9134 (mmm) cc_final: 0.8392 (mtp) REVERT: A 374 TYR cc_start: 0.6744 (m-80) cc_final: 0.5962 (m-80) REVERT: A 481 SER cc_start: 0.9610 (m) cc_final: 0.9310 (p) REVERT: A 504 LYS cc_start: 0.8927 (mttt) cc_final: 0.8501 (mmmt) REVERT: A 562 MET cc_start: 0.8801 (mmm) cc_final: 0.8168 (mmm) REVERT: A 601 ASP cc_start: 0.7589 (t0) cc_final: 0.7187 (p0) REVERT: A 648 GLU cc_start: 0.8510 (tt0) cc_final: 0.8004 (pp20) REVERT: A 716 MET cc_start: 0.8074 (tpp) cc_final: 0.7838 (tmm) REVERT: D 211 ARG cc_start: 0.9267 (mmt180) cc_final: 0.9038 (mpt90) REVERT: D 253 SER cc_start: 0.9274 (m) cc_final: 0.8865 (p) REVERT: D 351 TYR cc_start: 0.8867 (t80) cc_final: 0.8525 (t80) REVERT: D 369 PHE cc_start: 0.6802 (t80) cc_final: 0.6476 (t80) REVERT: D 383 ASP cc_start: 0.8157 (p0) cc_final: 0.7322 (t0) REVERT: D 406 THR cc_start: 0.8477 (m) cc_final: 0.8078 (p) REVERT: D 581 MET cc_start: 0.6377 (tpp) cc_final: 0.5451 (tpp) REVERT: D 585 LEU cc_start: 0.9315 (mt) cc_final: 0.9095 (mm) REVERT: D 700 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8463 (tm-30) REVERT: D 716 MET cc_start: 0.5848 (ttm) cc_final: 0.5330 (tpt) REVERT: B 228 GLN cc_start: 0.7917 (mp10) cc_final: 0.7656 (mp10) REVERT: B 293 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7697 (mt-10) REVERT: B 397 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8194 (mt-10) REVERT: B 513 GLU cc_start: 0.8348 (mp0) cc_final: 0.7869 (mt-10) REVERT: B 656 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8577 (tttp) REVERT: B 663 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8976 (mm) REVERT: B 725 LEU cc_start: 0.9356 (mp) cc_final: 0.9135 (mt) REVERT: C 228 GLN cc_start: 0.8452 (mt0) cc_final: 0.8198 (pm20) REVERT: C 294 VAL cc_start: 0.9395 (t) cc_final: 0.9143 (m) REVERT: C 308 MET cc_start: 0.9182 (mmm) cc_final: 0.8948 (mmm) REVERT: C 309 TYR cc_start: 0.9139 (t80) cc_final: 0.8810 (t80) REVERT: C 383 ASP cc_start: 0.8097 (t0) cc_final: 0.7848 (t0) REVERT: C 481 SER cc_start: 0.9625 (m) cc_final: 0.9257 (p) REVERT: C 562 MET cc_start: 0.8943 (mmm) cc_final: 0.8282 (mmp) REVERT: C 700 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8467 (tp-100) outliers start: 48 outliers final: 23 residues processed: 538 average time/residue: 0.1270 time to fit residues: 105.4312 Evaluate side-chains 496 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 471 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 656 LYS Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 677 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 86 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 153 optimal weight: 0.4980 chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 201 optimal weight: 3.9990 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 727 GLN D 228 GLN B 423 GLN C 423 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.126538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.095438 restraints weight = 38641.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.098412 restraints weight = 18871.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.100368 restraints weight = 12221.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.101597 restraints weight = 9362.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.102293 restraints weight = 7949.044| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 18033 Z= 0.150 Angle : 0.582 9.745 24463 Z= 0.302 Chirality : 0.039 0.184 2752 Planarity : 0.003 0.045 3012 Dihedral : 4.807 53.597 2761 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.27 % Allowed : 16.35 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 1.50 (0.19), residues: 2136 helix: 2.25 (0.14), residues: 1292 sheet: 0.30 (0.54), residues: 76 loop : -1.19 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.021 0.001 TYR A 666 PHE 0.019 0.001 PHE D 580 TRP 0.020 0.001 TRP B 372 HIS 0.004 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00347 (18032) covalent geometry : angle 0.58215 (24463) hydrogen bonds : bond 0.04270 ( 1010) hydrogen bonds : angle 3.83865 ( 2907) Misc. bond : bond 0.00047 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 487 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.7753 (t80) cc_final: 0.6999 (t80) REVERT: A 308 MET cc_start: 0.9146 (mmm) cc_final: 0.8344 (mtp) REVERT: A 481 SER cc_start: 0.9624 (m) cc_final: 0.9152 (p) REVERT: A 562 MET cc_start: 0.8861 (mmm) cc_final: 0.8211 (mmm) REVERT: A 601 ASP cc_start: 0.7603 (t0) cc_final: 0.7197 (p0) REVERT: A 648 GLU cc_start: 0.8520 (tt0) cc_final: 0.8086 (pp20) REVERT: A 737 ASP cc_start: 0.6091 (p0) cc_final: 0.5875 (p0) REVERT: D 253 SER cc_start: 0.9306 (m) cc_final: 0.8936 (p) REVERT: D 369 PHE cc_start: 0.6843 (t80) cc_final: 0.6432 (t80) REVERT: D 383 ASP cc_start: 0.8149 (p0) cc_final: 0.7364 (t0) REVERT: D 388 ASP cc_start: 0.8676 (p0) cc_final: 0.8465 (p0) REVERT: D 389 THR cc_start: 0.8471 (m) cc_final: 0.8258 (m) REVERT: D 406 THR cc_start: 0.8489 (m) cc_final: 0.8128 (p) REVERT: D 700 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8463 (tm-30) REVERT: D 716 MET cc_start: 0.5827 (ttm) cc_final: 0.5454 (tpt) REVERT: B 228 GLN cc_start: 0.7963 (mp10) cc_final: 0.7659 (mp10) REVERT: B 397 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8208 (mt-10) REVERT: B 513 GLU cc_start: 0.8400 (mp0) cc_final: 0.7900 (mt-10) REVERT: B 656 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8549 (tttp) REVERT: B 663 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9059 (mm) REVERT: B 725 LEU cc_start: 0.9369 (mp) cc_final: 0.9148 (mt) REVERT: C 228 GLN cc_start: 0.8427 (mt0) cc_final: 0.8156 (pm20) REVERT: C 308 MET cc_start: 0.9193 (mmm) cc_final: 0.8980 (mmm) REVERT: C 309 TYR cc_start: 0.9132 (t80) cc_final: 0.8782 (t80) REVERT: C 383 ASP cc_start: 0.8134 (t0) cc_final: 0.7924 (t0) REVERT: C 562 MET cc_start: 0.8969 (mmm) cc_final: 0.8486 (mmp) REVERT: C 700 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8457 (tp-100) outliers start: 62 outliers final: 42 residues processed: 514 average time/residue: 0.1246 time to fit residues: 99.5324 Evaluate side-chains 513 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 469 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 741 CYS Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 550 THR Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 656 LYS Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 677 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 124 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 155 optimal weight: 0.2980 chunk 10 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 228 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.122156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.091895 restraints weight = 38993.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.094658 restraints weight = 19067.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.096514 restraints weight = 12515.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.097668 restraints weight = 9646.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098235 restraints weight = 8227.987| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 18033 Z= 0.268 Angle : 0.672 10.819 24463 Z= 0.347 Chirality : 0.042 0.182 2752 Planarity : 0.004 0.045 3012 Dihedral : 5.183 55.082 2761 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.59 % Allowed : 16.67 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 1.17 (0.18), residues: 2136 helix: 2.00 (0.14), residues: 1292 sheet: -0.08 (0.54), residues: 76 loop : -1.32 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 409 TYR 0.022 0.002 TYR A 666 PHE 0.020 0.002 PHE A 559 TRP 0.023 0.001 TRP B 372 HIS 0.007 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00608 (18032) covalent geometry : angle 0.67197 (24463) hydrogen bonds : bond 0.05090 ( 1010) hydrogen bonds : angle 4.15440 ( 2907) Misc. bond : bond 0.00103 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 461 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.7717 (t80) cc_final: 0.6995 (t80) REVERT: A 308 MET cc_start: 0.9144 (mmm) cc_final: 0.8735 (tpp) REVERT: A 562 MET cc_start: 0.8923 (mmm) cc_final: 0.8297 (mmm) REVERT: A 581 MET cc_start: 0.7220 (tpp) cc_final: 0.6846 (tpp) REVERT: A 648 GLU cc_start: 0.8583 (tt0) cc_final: 0.8112 (pp20) REVERT: A 737 ASP cc_start: 0.5944 (p0) cc_final: 0.5702 (p0) REVERT: D 253 SER cc_start: 0.9325 (m) cc_final: 0.9017 (p) REVERT: D 383 ASP cc_start: 0.8032 (p0) cc_final: 0.7247 (t0) REVERT: D 406 THR cc_start: 0.8549 (m) cc_final: 0.8278 (p) REVERT: D 700 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8406 (tm-30) REVERT: D 716 MET cc_start: 0.5914 (ttm) cc_final: 0.5599 (tpt) REVERT: B 383 ASP cc_start: 0.8283 (t70) cc_final: 0.8067 (t70) REVERT: B 397 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8222 (mt-10) REVERT: B 420 ARG cc_start: 0.8818 (mmm-85) cc_final: 0.8603 (mmm160) REVERT: B 481 SER cc_start: 0.9501 (m) cc_final: 0.9259 (p) REVERT: B 491 ARG cc_start: 0.8997 (mmm-85) cc_final: 0.8752 (mmm-85) REVERT: B 511 TYR cc_start: 0.8886 (t80) cc_final: 0.8611 (t80) REVERT: B 656 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8483 (tttp) REVERT: B 663 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9015 (mm) REVERT: B 700 GLN cc_start: 0.9114 (tp-100) cc_final: 0.8773 (tp40) REVERT: C 228 GLN cc_start: 0.8379 (mt0) cc_final: 0.8087 (pm20) REVERT: C 700 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8526 (tp-100) REVERT: C 704 THR cc_start: 0.9488 (m) cc_final: 0.9266 (p) outliers start: 68 outliers final: 50 residues processed: 496 average time/residue: 0.1247 time to fit residues: 96.0626 Evaluate side-chains 491 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 439 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 378 HIS Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 550 THR Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 656 LYS Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 677 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 HIS ** B 228 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 = 0.3644 r_free = 0.3644 target = 0.126238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.096268 restraints weight = 38484.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099140 restraints weight = 18476.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.101104 restraints weight = 11930.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.102312 restraints weight = 9100.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102922 restraints weight = 7704.397| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18033 Z= 0.120 Angle : 0.609 11.872 24463 Z= 0.310 Chirality : 0.039 0.211 2752 Planarity : 0.004 0.045 3012 Dihedral : 4.623 53.380 2761 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.48 % Allowed : 18.78 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 1.41 (0.19), residues: 2136 helix: 2.23 (0.14), residues: 1284 sheet: 0.09 (0.58), residues: 76 loop : -1.27 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 491 TYR 0.020 0.001 TYR A 666 PHE 0.023 0.001 PHE D 266 TRP 0.027 0.001 TRP B 372 HIS 0.006 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00259 (18032) covalent geometry : angle 0.60868 (24463) hydrogen bonds : bond 0.04225 ( 1010) hydrogen bonds : angle 3.89248 ( 2907) Misc. bond : bond 0.00039 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 494 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.7802 (t80) cc_final: 0.7109 (t80) REVERT: A 308 MET cc_start: 0.9076 (mmm) cc_final: 0.8316 (mtp) REVERT: A 481 SER cc_start: 0.9634 (m) cc_final: 0.9177 (p) REVERT: A 562 MET cc_start: 0.8921 (mmm) cc_final: 0.8568 (mmm) REVERT: A 601 ASP cc_start: 0.7614 (t0) cc_final: 0.7182 (p0) REVERT: A 648 GLU cc_start: 0.8588 (tt0) cc_final: 0.8098 (pp20) REVERT: A 704 THR cc_start: 0.9346 (m) cc_final: 0.9141 (p) REVERT: A 737 ASP cc_start: 0.5835 (p0) cc_final: 0.5619 (p0) REVERT: D 211 ARG cc_start: 0.9312 (mmt180) cc_final: 0.8811 (mpt90) REVERT: D 253 SER cc_start: 0.9301 (m) cc_final: 0.8962 (p) REVERT: D 308 MET cc_start: 0.9119 (mmm) cc_final: 0.8873 (mmm) REVERT: D 383 ASP cc_start: 0.8140 (p0) cc_final: 0.7206 (t0) REVERT: D 384 LEU cc_start: 0.8548 (mt) cc_final: 0.8295 (mp) REVERT: D 406 THR cc_start: 0.8512 (m) cc_final: 0.8231 (p) REVERT: D 700 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8400 (tm-30) REVERT: D 716 MET cc_start: 0.5934 (ttm) cc_final: 0.5673 (tpt) REVERT: B 214 MET cc_start: 0.9042 (pmm) cc_final: 0.8757 (pmm) REVERT: B 383 ASP cc_start: 0.8229 (t70) cc_final: 0.7999 (t70) REVERT: B 397 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8186 (mt-10) REVERT: B 481 SER cc_start: 0.9495 (m) cc_final: 0.9260 (p) REVERT: B 491 ARG cc_start: 0.9018 (mmm-85) cc_final: 0.8723 (mmm-85) REVERT: B 513 GLU cc_start: 0.8429 (mp0) cc_final: 0.7954 (mt-10) REVERT: B 700 GLN cc_start: 0.9125 (tp-100) cc_final: 0.8771 (tp40) REVERT: C 228 GLN cc_start: 0.8379 (mt0) cc_final: 0.8141 (pm20) REVERT: C 246 TYR cc_start: 0.7175 (t80) cc_final: 0.6841 (t80) REVERT: C 261 LEU cc_start: 0.8910 (pt) cc_final: 0.8095 (tp) REVERT: C 308 MET cc_start: 0.9204 (mmm) cc_final: 0.8852 (mtp) REVERT: C 700 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8488 (tp-100) REVERT: C 704 THR cc_start: 0.9449 (m) cc_final: 0.9191 (p) outliers start: 47 outliers final: 29 residues processed: 512 average time/residue: 0.1224 time to fit residues: 97.8407 Evaluate side-chains 496 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 467 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 541 MET Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 677 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 120 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 151 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 201 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 HIS ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.126463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.096593 restraints weight = 38582.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099479 restraints weight = 18717.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.101468 restraints weight = 12071.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.102675 restraints weight = 9173.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.103305 restraints weight = 7759.851| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18033 Z= 0.119 Angle : 0.608 11.286 24463 Z= 0.308 Chirality : 0.039 0.208 2752 Planarity : 0.003 0.042 3012 Dihedral : 4.312 48.496 2757 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.90 % Allowed : 20.25 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 1.43 (0.19), residues: 2136 helix: 2.23 (0.14), residues: 1284 sheet: 0.31 (0.60), residues: 76 loop : -1.27 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 739 TYR 0.023 0.001 TYR D 666 PHE 0.020 0.001 PHE B 649 TRP 0.028 0.001 TRP B 372 HIS 0.003 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00262 (18032) covalent geometry : angle 0.60759 (24463) hydrogen bonds : bond 0.04070 ( 1010) hydrogen bonds : angle 3.88475 ( 2907) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 486 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.7832 (t80) cc_final: 0.7461 (t80) REVERT: A 308 MET cc_start: 0.9085 (mmm) cc_final: 0.8705 (tpp) REVERT: A 481 SER cc_start: 0.9565 (m) cc_final: 0.9213 (p) REVERT: A 562 MET cc_start: 0.8958 (mmm) cc_final: 0.8623 (mmm) REVERT: A 571 LYS cc_start: 0.9276 (mtpp) cc_final: 0.9018 (mtmm) REVERT: A 601 ASP cc_start: 0.7507 (t0) cc_final: 0.7124 (p0) REVERT: A 648 GLU cc_start: 0.8581 (tt0) cc_final: 0.8122 (pp20) REVERT: A 704 THR cc_start: 0.9302 (m) cc_final: 0.9065 (p) REVERT: A 737 ASP cc_start: 0.5786 (p0) cc_final: 0.5534 (p0) REVERT: D 211 ARG cc_start: 0.9301 (mmt180) cc_final: 0.8839 (mpt90) REVERT: D 253 SER cc_start: 0.9350 (m) cc_final: 0.9029 (p) REVERT: D 351 TYR cc_start: 0.9018 (t80) cc_final: 0.8720 (t80) REVERT: D 383 ASP cc_start: 0.8204 (p0) cc_final: 0.7245 (t0) REVERT: D 384 LEU cc_start: 0.8654 (mt) cc_final: 0.8349 (mp) REVERT: D 406 THR cc_start: 0.8449 (m) cc_final: 0.8192 (p) REVERT: D 585 LEU cc_start: 0.9350 (mt) cc_final: 0.9077 (mm) REVERT: D 716 MET cc_start: 0.5925 (ttm) cc_final: 0.5647 (tpt) REVERT: B 214 MET cc_start: 0.9030 (pmm) cc_final: 0.8730 (pmm) REVERT: B 383 ASP cc_start: 0.8200 (t70) cc_final: 0.7970 (t70) REVERT: B 397 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8275 (mt-10) REVERT: B 481 SER cc_start: 0.9463 (m) cc_final: 0.9249 (p) REVERT: B 491 ARG cc_start: 0.9007 (mmm-85) cc_final: 0.8748 (mmm-85) REVERT: B 700 GLN cc_start: 0.9096 (tp-100) cc_final: 0.8655 (tp40) REVERT: C 228 GLN cc_start: 0.8389 (mt0) cc_final: 0.8152 (pm20) REVERT: C 246 TYR cc_start: 0.7207 (t80) cc_final: 0.6900 (t80) REVERT: C 383 ASP cc_start: 0.8055 (t70) cc_final: 0.7786 (t70) REVERT: C 700 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8473 (tp-100) REVERT: C 704 THR cc_start: 0.9431 (m) cc_final: 0.9164 (p) outliers start: 36 outliers final: 27 residues processed: 499 average time/residue: 0.1250 time to fit residues: 97.6267 Evaluate side-chains 503 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 476 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 386 CYS Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 677 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 207 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 172 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.127000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.097090 restraints weight = 38720.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.099961 restraints weight = 18789.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.101927 restraints weight = 12075.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.103134 restraints weight = 9207.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.103919 restraints weight = 7804.124| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18033 Z= 0.122 Angle : 0.638 14.152 24463 Z= 0.319 Chirality : 0.039 0.233 2752 Planarity : 0.003 0.045 3012 Dihedral : 4.261 48.424 2757 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.69 % Allowed : 20.83 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 1.42 (0.19), residues: 2136 helix: 2.19 (0.14), residues: 1284 sheet: 0.51 (0.62), residues: 76 loop : -1.24 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 420 TYR 0.019 0.001 TYR B 309 PHE 0.025 0.001 PHE A 712 TRP 0.031 0.001 TRP B 372 HIS 0.003 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00272 (18032) covalent geometry : angle 0.63799 (24463) hydrogen bonds : bond 0.04006 ( 1010) hydrogen bonds : angle 3.89352 ( 2907) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 483 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.7833 (t80) cc_final: 0.7248 (t80) REVERT: A 308 MET cc_start: 0.9085 (mmm) cc_final: 0.8274 (mtp) REVERT: A 481 SER cc_start: 0.9615 (m) cc_final: 0.9180 (p) REVERT: A 562 MET cc_start: 0.8993 (mmm) cc_final: 0.8667 (mmm) REVERT: A 571 LYS cc_start: 0.9281 (mtpp) cc_final: 0.9015 (mtmm) REVERT: A 601 ASP cc_start: 0.7460 (t0) cc_final: 0.7093 (p0) REVERT: A 648 GLU cc_start: 0.8593 (tt0) cc_final: 0.8140 (pp20) REVERT: D 211 ARG cc_start: 0.9296 (mmt180) cc_final: 0.8835 (mpt90) REVERT: D 253 SER cc_start: 0.9366 (m) cc_final: 0.9046 (p) REVERT: D 351 TYR cc_start: 0.9024 (t80) cc_final: 0.8732 (t80) REVERT: D 383 ASP cc_start: 0.8212 (p0) cc_final: 0.7272 (t0) REVERT: D 384 LEU cc_start: 0.8661 (mt) cc_final: 0.8375 (mp) REVERT: D 406 THR cc_start: 0.8434 (m) cc_final: 0.8160 (p) REVERT: D 585 LEU cc_start: 0.9345 (mt) cc_final: 0.9141 (mm) REVERT: B 214 MET cc_start: 0.9031 (pmm) cc_final: 0.8727 (pmm) REVERT: B 383 ASP cc_start: 0.8182 (t70) cc_final: 0.7949 (t70) REVERT: B 386 CYS cc_start: 0.9114 (m) cc_final: 0.8097 (t) REVERT: B 397 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8329 (mt-10) REVERT: B 491 ARG cc_start: 0.9000 (mmm-85) cc_final: 0.8729 (mmm-85) REVERT: B 700 GLN cc_start: 0.9105 (tp-100) cc_final: 0.8660 (tp40) REVERT: C 228 GLN cc_start: 0.8369 (mt0) cc_final: 0.8152 (pm20) REVERT: C 246 TYR cc_start: 0.7272 (t80) cc_final: 0.6960 (t80) REVERT: C 397 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8121 (mt-10) REVERT: C 700 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8446 (tp-100) outliers start: 32 outliers final: 28 residues processed: 495 average time/residue: 0.1289 time to fit residues: 98.5554 Evaluate side-chains 497 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 469 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 405 GLU Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 677 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 58 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 185 optimal weight: 0.0040 chunk 142 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 10 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.126821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.096974 restraints weight = 38743.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.099828 restraints weight = 18881.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.101807 restraints weight = 12145.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.103012 restraints weight = 9246.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103657 restraints weight = 7831.011| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18033 Z= 0.124 Angle : 0.633 15.204 24463 Z= 0.318 Chirality : 0.040 0.229 2752 Planarity : 0.003 0.042 3012 Dihedral : 4.221 48.740 2757 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.69 % Allowed : 21.36 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 1.39 (0.19), residues: 2136 helix: 2.17 (0.14), residues: 1284 sheet: 0.58 (0.63), residues: 76 loop : -1.26 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 428 TYR 0.020 0.001 TYR A 309 PHE 0.022 0.001 PHE A 712 TRP 0.030 0.001 TRP B 372 HIS 0.004 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00275 (18032) covalent geometry : angle 0.63285 (24463) hydrogen bonds : bond 0.04013 ( 1010) hydrogen bonds : angle 3.91917 ( 2907) Misc. bond : bond 0.00033 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 479 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 PHE cc_start: 0.7812 (t80) cc_final: 0.7470 (t80) REVERT: A 308 MET cc_start: 0.9084 (mmm) cc_final: 0.8701 (tpp) REVERT: A 481 SER cc_start: 0.9543 (m) cc_final: 0.9209 (p) REVERT: A 562 MET cc_start: 0.9011 (mmm) cc_final: 0.8791 (mmm) REVERT: A 571 LYS cc_start: 0.9287 (mtpp) cc_final: 0.9030 (mtmm) REVERT: A 601 ASP cc_start: 0.7484 (t0) cc_final: 0.7129 (p0) REVERT: A 648 GLU cc_start: 0.8596 (tt0) cc_final: 0.8115 (pp20) REVERT: D 253 SER cc_start: 0.9351 (m) cc_final: 0.9033 (p) REVERT: D 351 TYR cc_start: 0.9032 (t80) cc_final: 0.8725 (t80) REVERT: D 383 ASP cc_start: 0.8212 (p0) cc_final: 0.7198 (t0) REVERT: D 384 LEU cc_start: 0.8667 (mt) cc_final: 0.8376 (mp) REVERT: D 406 THR cc_start: 0.8410 (m) cc_final: 0.8101 (p) REVERT: D 585 LEU cc_start: 0.9349 (mt) cc_final: 0.9117 (mm) REVERT: B 214 MET cc_start: 0.9046 (pmm) cc_final: 0.8740 (pmm) REVERT: B 383 ASP cc_start: 0.8181 (t70) cc_final: 0.7950 (t70) REVERT: B 386 CYS cc_start: 0.9137 (m) cc_final: 0.8137 (t) REVERT: B 491 ARG cc_start: 0.9009 (mmm-85) cc_final: 0.8731 (mmm-85) REVERT: B 503 LEU cc_start: 0.9122 (mm) cc_final: 0.8860 (tt) REVERT: B 700 GLN cc_start: 0.9104 (tp-100) cc_final: 0.8658 (tp40) REVERT: C 228 GLN cc_start: 0.8376 (mt0) cc_final: 0.8162 (pm20) REVERT: C 246 TYR cc_start: 0.7280 (t80) cc_final: 0.6957 (t80) REVERT: C 397 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8120 (mt-10) REVERT: C 423 GLN cc_start: 0.8522 (tp40) cc_final: 0.8238 (tp-100) REVERT: C 700 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8446 (tp-100) outliers start: 32 outliers final: 27 residues processed: 493 average time/residue: 0.1278 time to fit residues: 98.9756 Evaluate side-chains 498 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 471 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 561 GLN Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 677 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 171 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 147 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.126680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.096761 restraints weight = 39016.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099629 restraints weight = 18878.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.101595 restraints weight = 12194.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.102809 restraints weight = 9296.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.103358 restraints weight = 7857.932| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 18033 Z= 0.130 Angle : 0.648 15.410 24463 Z= 0.324 Chirality : 0.041 0.325 2752 Planarity : 0.003 0.044 3012 Dihedral : 4.217 50.012 2757 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.58 % Allowed : 21.62 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 1.35 (0.19), residues: 2136 helix: 2.13 (0.14), residues: 1284 sheet: 0.55 (0.63), residues: 76 loop : -1.27 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 428 TYR 0.019 0.001 TYR A 309 PHE 0.021 0.001 PHE A 712 TRP 0.030 0.001 TRP B 372 HIS 0.004 0.001 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00298 (18032) covalent geometry : angle 0.64833 (24463) hydrogen bonds : bond 0.04052 ( 1010) hydrogen bonds : angle 3.97970 ( 2907) Misc. bond : bond 0.00037 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3379.60 seconds wall clock time: 59 minutes 2.48 seconds (3542.48 seconds total)