Starting phenix.real_space_refine on Sat Jul 4 03:05:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7l2v_23142/07_2026/7l2v_23142.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l2v_23142/07_2026/7l2v_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 { model { file = "/net/cci-nas-00/data/ceres_data/7l2v_23142/07_2026/7l2v_23142.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l2v_23142/07_2026/7l2v_23142.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7l2v_23142/07_2026/7l2v_23142.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7l2v_23142/07_2026/7l2v_23142.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l2v_23142/07_2026/7l2v_23142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l2v_23142/07_2026/7l2v_23142.map" } 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-dev-6108/lib/python3.11/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: 3.80, per 1000 atoms: 0.22 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: 1.67 Conformation dependent library (CDL) restraints added in 782.5 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: 0.46 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: 2.91 Time building geometry restraints manager: 2.12 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: 9842 16.06 - 32.12: 571 32.12 - 48.18: 68 48.18 - 64.24: 29 64.24 - 80.30: 15 Dihedral angle restraints: 10525 sinusoidal: 4205 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 10522 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: 2.440 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.500 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 11.079 80.300 6469 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/Z covalent geometry : bond 0.00731 / 0.34 (18032) covalent geometry : angle 0.84993 / 0.45 (24463) hydrogen bonds : bond 0.14123 / 9.03 ( 1010) hydrogen bonds : angle 5.03387 / 3.62 ( 2907) Misc. bond : bond 0.88149 / 46.39 ( 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 : 0.678 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: 0.7943 (p0) cc_final: 0.7514 (t0) REVERT: D 406 THR cc_start: 0.8435 (m) cc_final: 0.8122 (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: 0.9153 (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: 0.8256 (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: 0.7844 (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: 0.8025 (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: 0.8593 (mt-10) cc_final: 0.8298 (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: 0.7538 (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: 0.8834 (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: 0.1382 time to fit residues: 150.7033 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 : 0.595 ------------------------------------------------------------------------------- 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... 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 = 0.3670 r_free = 0.3670 target = 0.127535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.097266 restraints weight = 38304.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.100317 restraints weight = 18375.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.102363 restraints weight = 11755.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103361 restraints weight = 8931.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.104376 restraints weight = 7719.357| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2823 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 : 0.616 6.736 24463 Z= 0.325 Chirality : 0.040 0.194 2752 Planarity : 0.004 0.040 3012 Dihedral : 5.282 55.692 2401 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.95 % Allowed : 10.76 % Favored : 87.29 % 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: 1.40 (0.18), residues: 2136 helix: 2.16 (0.14), residues: 1284 sheet: -0.26 (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 0.023 0.001 TRP B 740 HIS 0.002 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (18032) covalent geometry : angle 0.61646 / 0.33 (24463) hydrogen bonds : bond 0.05130 / 3.36 ( 1010) hydrogen bonds : angle 3.94748 / 2.82 ( 2907) Misc. bond : bond 0.00542 / 0.29 ( 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 : 0.597 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 308 MET cc_start: 0.9012 (mmm) cc_final: 0.8402 (mtp) REVERT: A 374 TYR cc_start: 0.6624 (m-80) cc_final: 0.5562 (m-80) REVERT: A 504 LYS cc_start: 0.8881 (mttt) cc_final: 0.8493 (mmmt) REVERT: A 536 GLU cc_start: 0.8564 (mp0) cc_final: 0.8167 (mp0) REVERT: A 648 GLU cc_start: 0.8470 (tt0) cc_final: 0.8013 (pp20) REVERT: D 250 LEU cc_start: 0.8540 (mt) cc_final: 0.8304 (mt) REVERT: D 253 SER cc_start: 0.9288 (m) cc_final: 0.8784 (p) REVERT: D 308 MET cc_start: 0.9170 (mmm) cc_final: 0.8944 (mmm) REVERT: D 332 LYS cc_start: 0.9451 (mmmm) cc_final: 0.9211 (mtmm) REVERT: D 369 PHE cc_start: 0.6774 (t80) cc_final: 0.6476 (t80) REVERT: D 383 ASP cc_start: 0.8052 (p0) cc_final: 0.7499 (t0) REVERT: D 406 THR cc_start: 0.8412 (m) cc_final: 0.8116 (p) REVERT: B 202 GLN cc_start: 0.8524 (tt0) cc_final: 0.8124 (tt0) REVERT: B 211 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8772 (mmm-85) REVERT: B 228 GLN cc_start: 0.7936 (mp10) cc_final: 0.7697 (mp10) REVERT: B 293 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7666 (mt-10) REVERT: B 378 HIS cc_start: 0.8178 (p90) cc_final: 0.7261 (p-80) REVERT: B 397 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8079 (mt-10) REVERT: B 423 GLN cc_start: 0.8634 (tp40) cc_final: 0.8398 (tp-100) REVERT: B 513 GLU cc_start: 0.8318 (mp0) cc_final: 0.7931 (mt-10) REVERT: B 656 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8648 (tttm) REVERT: B 700 GLN cc_start: 0.8958 (tp40) cc_final: 0.8598 (tp40) REVERT: C 203 THR cc_start: 0.8099 (t) cc_final: 0.7188 (p) REVERT: C 219 LEU cc_start: 0.9575 (tp) cc_final: 0.9274 (tp) REVERT: C 222 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8550 (mt-10) REVERT: C 228 GLN cc_start: 0.8429 (mt0) cc_final: 0.8177 (pm20) REVERT: C 309 TYR cc_start: 0.9174 (t80) cc_final: 0.8929 (t80) REVERT: C 378 HIS cc_start: 0.7769 (p-80) cc_final: 0.7393 (p90) REVERT: C 403 SER cc_start: 0.8593 (p) cc_final: 0.8125 (m) REVERT: C 423 GLN cc_start: 0.8688 (tp40) cc_final: 0.8475 (tp-100) REVERT: C 481 SER cc_start: 0.9581 (m) cc_final: 0.9123 (p) REVERT: C 562 MET cc_start: 0.8946 (mmm) cc_final: 0.8424 (mmp) REVERT: C 700 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8569 (tp-100) REVERT: C 746 GLU cc_start: 0.7762 (pt0) cc_final: 0.7298 (pt0) outliers start: 37 outliers final: 20 residues processed: 569 average time/residue: 0.1193 time to fit residues: 104.0133 Evaluate side-chains 510 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 488 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 677 MET 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: 3.9990 chunk 33 optimal weight: 1.9990 chunk 159 optimal weight: 20.0000 chunk 178 optimal weight: 1.9990 chunk 185 optimal weight: 0.0970 chunk 0 optimal weight: 20.0000 chunk 40 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 206 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3653 r_free = 0.3653 target = 0.126778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.095764 restraints weight = 38886.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.098812 restraints weight = 18816.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.100837 restraints weight = 12060.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.102135 restraints weight = 9149.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.102775 restraints weight = 7725.388| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18033 Z= 0.137 Angle : 0.590 10.526 24463 Z= 0.308 Chirality : 0.039 0.271 2752 Planarity : 0.004 0.048 3012 Dihedral : 5.019 58.507 2401 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.01 % Allowed : 13.13 % Favored : 83.86 % 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: 1.47 (0.18), residues: 2136 helix: 2.23 (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 0.013 0.000 ARG C 211 TYR 0.015 0.001 TYR A 666 PHE 0.023 0.001 PHE C 304 TRP 0.013 0.001 TRP B 740 HIS 0.005 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (18032) covalent geometry : angle 0.58994 / 0.31 (24463) hydrogen bonds : bond 0.04570 / 2.98 ( 1010) hydrogen bonds : angle 3.84516 / 2.73 ( 2907) Misc. bond : bond 0.00045 / 0.02 ( 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 573 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 516 time to evaluate : 0.698 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: 0.7929 (tt0) cc_final: 0.7240 (tm-30) REVERT: A 304 PHE cc_start: 0.7657 (t80) cc_final: 0.6600 (t80) REVERT: A 308 MET cc_start: 0.9068 (mmm) cc_final: 0.8443 (mtp) REVERT: A 374 TYR cc_start: 0.6793 (m-80) cc_final: 0.6061 (m-80) REVERT: A 481 SER cc_start: 0.9627 (m) cc_final: 0.9183 (p) REVERT: A 504 LYS cc_start: 0.8916 (mttt) cc_final: 0.8497 (mmmt) REVERT: A 562 MET cc_start: 0.8795 (mmm) cc_final: 0.8205 (mmm) REVERT: A 648 GLU cc_start: 0.8526 (tt0) cc_final: 0.8030 (pp20) REVERT: A 697 TRP cc_start: 0.8622 (t60) cc_final: 0.8412 (t60) REVERT: D 211 ARG cc_start: 0.9305 (mmt180) cc_final: 0.9041 (mpt90) REVERT: D 253 SER cc_start: 0.9287 (m) cc_final: 0.8883 (p) REVERT: D 308 MET cc_start: 0.9224 (mmm) cc_final: 0.8983 (mmm) REVERT: D 369 PHE cc_start: 0.6820 (t80) cc_final: 0.6495 (t80) REVERT: D 383 ASP cc_start: 0.8098 (p0) cc_final: 0.7435 (t0) REVERT: D 406 THR cc_start: 0.8415 (m) cc_final: 0.8131 (p) REVERT: D 552 MET cc_start: 0.8941 (tpp) cc_final: 0.8739 (tpp) REVERT: B 228 GLN cc_start: 0.7932 (mp10) cc_final: 0.7688 (mp10) REVERT: B 293 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7676 (mt-10) REVERT: B 397 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8171 (mt-10) REVERT: B 423 GLN cc_start: 0.8662 (tp40) cc_final: 0.8421 (tp-100) REVERT: B 491 ARG cc_start: 0.9010 (mmm-85) cc_final: 0.8749 (mmm-85) REVERT: B 513 GLU cc_start: 0.8351 (mp0) cc_final: 0.7900 (mt-10) REVERT: B 570 GLU cc_start: 0.8494 (tt0) cc_final: 0.8271 (tt0) REVERT: B 656 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8619 (tttp) REVERT: B 700 GLN cc_start: 0.9016 (tp40) cc_final: 0.8724 (tp40) REVERT: C 213 ASN cc_start: 0.8725 (t0) cc_final: 0.8504 (t0) REVERT: C 219 LEU cc_start: 0.9518 (tp) cc_final: 0.9209 (tp) REVERT: C 222 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8482 (mt-10) REVERT: C 228 GLN cc_start: 0.8433 (mt0) cc_final: 0.8162 (pm20) REVERT: C 294 VAL cc_start: 0.9388 (t) cc_final: 0.9143 (m) REVERT: C 308 MET cc_start: 0.9178 (mmm) cc_final: 0.8795 (mtp) REVERT: C 309 TYR cc_start: 0.9174 (t80) cc_final: 0.8921 (t80) REVERT: C 383 ASP cc_start: 0.8137 (t0) cc_final: 0.7872 (t0) REVERT: C 481 SER cc_start: 0.9596 (m) cc_final: 0.9158 (p) REVERT: C 562 MET cc_start: 0.8920 (mmm) cc_final: 0.8613 (mmp) REVERT: C 700 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8776 (mm-40) outliers start: 57 outliers final: 32 residues processed: 541 average time/residue: 0.1079 time to fit residues: 90.5152 Evaluate side-chains 514 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 481 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 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 493 ILE 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 677 MET 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 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: 3.9990 chunk 47 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 198 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 HIS A 727 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 = 0.3661 r_free = 0.3661 target = 0.127506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.096967 restraints weight = 38812.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099993 restraints weight = 18577.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.101985 restraints weight = 11868.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.103239 restraints weight = 9035.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.104025 restraints weight = 7644.991| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18033 Z= 0.123 Angle : 0.585 11.865 24463 Z= 0.301 Chirality : 0.038 0.189 2752 Planarity : 0.003 0.041 3012 Dihedral : 4.847 57.670 2401 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.74 % Allowed : 15.66 % Favored : 81.59 % 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: 1.51 (0.19), residues: 2136 helix: 2.25 (0.14), residues: 1292 sheet: 0.19 (0.54), residues: 76 loop : -1.18 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 701 TYR 0.021 0.001 TYR A 666 PHE 0.020 0.001 PHE D 580 TRP 0.014 0.001 TRP B 740 HIS 0.007 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (18032) covalent geometry : angle 0.58524 / 0.30 (24463) hydrogen bonds : bond 0.04186 / 2.75 ( 1010) hydrogen bonds : angle 3.78663 / 2.69 ( 2907) Misc. bond : bond 0.00038 / 0.02 ( 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 563 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 511 time to evaluate : 0.701 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: 0.7869 (tt0) cc_final: 0.7344 (tm-30) REVERT: A 304 PHE cc_start: 0.7702 (t80) cc_final: 0.6944 (t80) REVERT: A 308 MET cc_start: 0.9133 (mmm) cc_final: 0.8408 (mtp) REVERT: A 374 TYR cc_start: 0.6771 (m-80) cc_final: 0.5980 (m-80) REVERT: A 481 SER cc_start: 0.9609 (m) cc_final: 0.9298 (p) REVERT: A 504 LYS cc_start: 0.8910 (mttt) cc_final: 0.8507 (mmmt) REVERT: A 562 MET cc_start: 0.8800 (mmm) cc_final: 0.8176 (mmm) REVERT: A 648 GLU cc_start: 0.8512 (tt0) cc_final: 0.8033 (pp20) REVERT: A 716 MET cc_start: 0.8048 (tpp) cc_final: 0.7825 (tmm) REVERT: D 211 ARG cc_start: 0.9250 (mmt180) cc_final: 0.9023 (mpt90) REVERT: D 253 SER cc_start: 0.9297 (m) cc_final: 0.8888 (p) REVERT: D 369 PHE cc_start: 0.6843 (t80) cc_final: 0.6465 (t80) REVERT: D 383 ASP cc_start: 0.8155 (p0) cc_final: 0.7348 (t0) REVERT: D 406 THR cc_start: 0.8483 (m) cc_final: 0.8099 (p) REVERT: D 581 MET cc_start: 0.6403 (tpp) cc_final: 0.5494 (tpp) REVERT: D 585 LEU cc_start: 0.9338 (mt) cc_final: 0.9105 (mm) REVERT: D 700 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8466 (tm-30) REVERT: D 716 MET cc_start: 0.5767 (ttm) cc_final: 0.5328 (tpt) REVERT: B 228 GLN cc_start: 0.7940 (mp10) cc_final: 0.7671 (mp10) REVERT: B 397 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8188 (mt-10) REVERT: B 423 GLN cc_start: 0.8690 (tp40) cc_final: 0.8487 (tp-100) REVERT: B 513 GLU cc_start: 0.8364 (mp0) cc_final: 0.7889 (mt-10) REVERT: B 656 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8586 (tttp) REVERT: B 663 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9030 (mm) REVERT: B 725 LEU cc_start: 0.9362 (mp) cc_final: 0.9148 (mt) REVERT: C 228 GLN cc_start: 0.8440 (mt0) cc_final: 0.8173 (pm20) REVERT: C 294 VAL cc_start: 0.9396 (t) cc_final: 0.9154 (m) REVERT: C 308 MET cc_start: 0.9178 (mmm) cc_final: 0.8954 (mmm) REVERT: C 309 TYR cc_start: 0.9186 (t80) cc_final: 0.8852 (t80) REVERT: C 383 ASP cc_start: 0.8103 (t0) cc_final: 0.7884 (t0) REVERT: C 481 SER cc_start: 0.9614 (m) cc_final: 0.9201 (p) REVERT: C 562 MET cc_start: 0.8956 (mmm) cc_final: 0.8541 (mmp) REVERT: C 700 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8496 (tp-100) outliers start: 52 outliers final: 27 residues processed: 531 average time/residue: 0.1114 time to fit residues: 92.8140 Evaluate side-chains 503 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 474 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 386 CYS Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 544 SER 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 635 LEU Chi-restraints excluded: chain D residue 641 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 686 VAL 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 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: 0.6980 chunk 192 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 201 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 727 GLN D 378 HIS C 423 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.126442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.095479 restraints weight = 38538.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.098492 restraints weight = 18540.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.100440 restraints weight = 11945.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.101649 restraints weight = 9149.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.102089 restraints weight = 7778.643| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18033 Z= 0.153 Angle : 0.584 10.015 24463 Z= 0.303 Chirality : 0.039 0.185 2752 Planarity : 0.004 0.044 3012 Dihedral : 4.774 57.535 2401 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.11 % Allowed : 16.35 % Favored : 80.54 % 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: 1.48 (0.19), residues: 2136 helix: 2.24 (0.14), residues: 1292 sheet: 0.19 (0.54), residues: 76 loop : -1.20 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 420 TYR 0.022 0.001 TYR A 666 PHE 0.019 0.001 PHE D 580 TRP 0.020 0.001 TRP B 372 HIS 0.003 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (18032) covalent geometry : angle 0.58427 / 0.30 (24463) hydrogen bonds : bond 0.04330 / 2.86 ( 1010) hydrogen bonds : angle 3.83347 / 2.72 ( 2907) Misc. bond : bond 0.00036 / 0.02 ( 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 552 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 493 time to evaluate : 0.669 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: 0.7731 (t80) cc_final: 0.6956 (t80) REVERT: A 308 MET cc_start: 0.9146 (mmm) cc_final: 0.8341 (mtp) REVERT: A 481 SER cc_start: 0.9641 (m) cc_final: 0.9260 (p) REVERT: A 601 ASP cc_start: 0.7648 (t0) cc_final: 0.7217 (p0) REVERT: A 648 GLU cc_start: 0.8527 (tt0) cc_final: 0.8075 (pp20) REVERT: A 737 ASP cc_start: 0.6086 (p0) cc_final: 0.5878 (p0) REVERT: D 211 ARG cc_start: 0.9266 (mmt180) cc_final: 0.9028 (mpt90) REVERT: D 253 SER cc_start: 0.9302 (m) cc_final: 0.8930 (p) REVERT: D 308 MET cc_start: 0.9206 (mmm) cc_final: 0.8922 (mmm) REVERT: D 351 TYR cc_start: 0.8949 (t80) cc_final: 0.8603 (t80) REVERT: D 369 PHE cc_start: 0.6867 (t80) cc_final: 0.6453 (t80) REVERT: D 383 ASP cc_start: 0.8152 (p0) cc_final: 0.7373 (t0) REVERT: D 389 THR cc_start: 0.8463 (m) cc_final: 0.8233 (m) REVERT: D 406 THR cc_start: 0.8494 (m) cc_final: 0.8147 (p) REVERT: D 716 MET cc_start: 0.5783 (ttm) cc_final: 0.5384 (tpt) REVERT: B 228 GLN cc_start: 0.7944 (mp10) cc_final: 0.7641 (mp10) REVERT: B 372 TRP cc_start: 0.7925 (p-90) cc_final: 0.7634 (p-90) REVERT: B 397 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8190 (mt-10) REVERT: B 513 GLU cc_start: 0.8414 (mp0) cc_final: 0.7922 (mt-10) REVERT: B 656 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8547 (tttp) REVERT: B 663 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9086 (mm) REVERT: B 725 LEU cc_start: 0.9368 (mp) cc_final: 0.9152 (mt) REVERT: C 228 GLN cc_start: 0.8444 (mt0) cc_final: 0.8160 (pm20) REVERT: C 246 TYR cc_start: 0.7015 (t80) cc_final: 0.6794 (t80) REVERT: C 308 MET cc_start: 0.9201 (mmm) cc_final: 0.8988 (mmm) REVERT: C 309 TYR cc_start: 0.9126 (t80) cc_final: 0.8776 (t80) REVERT: C 383 ASP cc_start: 0.8133 (t0) cc_final: 0.7917 (t0) REVERT: C 562 MET cc_start: 0.8980 (mmm) cc_final: 0.8495 (mmp) REVERT: C 700 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8486 (tp-100) outliers start: 59 outliers final: 42 residues processed: 520 average time/residue: 0.1143 time to fit residues: 93.0282 Evaluate side-chains 512 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 468 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 322 THR Chi-restraints excluded: chain A residue 386 CYS Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 483 SER 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 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 677 MET 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 414 LEU 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 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 386 CYS Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 506 LEU 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: 5.9990 chunk 118 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 chunk 162 optimal weight: 20.0000 chunk 145 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.125482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.095323 restraints weight = 38473.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.098195 restraints weight = 18795.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.100119 restraints weight = 12153.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.101334 restraints weight = 9296.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.101921 restraints weight = 7871.464| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18033 Z= 0.151 Angle : 0.589 10.703 24463 Z= 0.303 Chirality : 0.039 0.192 2752 Planarity : 0.003 0.041 3012 Dihedral : 4.687 53.003 2401 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.95 % Allowed : 17.41 % Favored : 79.64 % 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: 2.26 (0.14), residues: 1292 sheet: 0.22 (0.55), residues: 76 loop : -1.23 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 499 TYR 0.021 0.001 TYR A 666 PHE 0.017 0.001 PHE D 580 TRP 0.019 0.001 TRP B 372 HIS 0.009 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (18032) covalent geometry : angle 0.58856 / 0.30 (24463) hydrogen bonds : bond 0.04262 / 2.81 ( 1010) hydrogen bonds : angle 3.87468 / 2.75 ( 2907) Misc. bond : bond 0.00041 / 0.02 ( 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 536 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 480 time to evaluate : 0.755 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: 0.7709 (t80) cc_final: 0.6949 (t80) REVERT: A 308 MET cc_start: 0.9136 (mmm) cc_final: 0.8333 (mtp) REVERT: A 562 MET cc_start: 0.8808 (mmm) cc_final: 0.8469 (mmm) REVERT: A 601 ASP cc_start: 0.7598 (t0) cc_final: 0.7201 (p0) REVERT: A 648 GLU cc_start: 0.8581 (tt0) cc_final: 0.8098 (pp20) REVERT: A 716 MET cc_start: 0.8143 (tpp) cc_final: 0.7422 (mtm) REVERT: A 737 ASP cc_start: 0.5945 (p0) cc_final: 0.5693 (p0) REVERT: D 253 SER cc_start: 0.9325 (m) cc_final: 0.8986 (p) REVERT: D 369 PHE cc_start: 0.6919 (t80) cc_final: 0.6478 (t80) REVERT: D 378 HIS cc_start: 0.8217 (OUTLIER) cc_final: 0.7238 (m90) REVERT: D 383 ASP cc_start: 0.8150 (p0) cc_final: 0.7290 (t0) REVERT: D 406 THR cc_start: 0.8524 (m) cc_final: 0.8210 (p) REVERT: D 716 MET cc_start: 0.5806 (ttm) cc_final: 0.5441 (tpt) REVERT: B 372 TRP cc_start: 0.7982 (p-90) cc_final: 0.7771 (p-90) REVERT: B 383 ASP cc_start: 0.8222 (t70) cc_final: 0.7998 (t70) REVERT: B 397 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8169 (mt-10) REVERT: B 481 SER cc_start: 0.9486 (m) cc_final: 0.9252 (p) REVERT: B 491 ARG cc_start: 0.9026 (mmm-85) cc_final: 0.8731 (mmm-85) REVERT: B 656 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8479 (tttp) REVERT: B 663 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9087 (mm) REVERT: C 228 GLN cc_start: 0.8422 (mt0) cc_final: 0.8135 (pm20) REVERT: C 246 TYR cc_start: 0.7039 (t80) cc_final: 0.6680 (t80) REVERT: C 309 TYR cc_start: 0.9114 (t80) cc_final: 0.8742 (t80) REVERT: C 383 ASP cc_start: 0.8162 (t0) cc_final: 0.7954 (t0) REVERT: C 562 MET cc_start: 0.8953 (mmm) cc_final: 0.8381 (mmp) REVERT: C 700 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8509 (tp-100) outliers start: 56 outliers final: 40 residues processed: 506 average time/residue: 0.1128 time to fit residues: 89.2011 Evaluate side-chains 515 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 472 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 386 CYS Chi-restraints excluded: chain A residue 483 SER 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 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 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 219 LEU Chi-restraints excluded: chain B residue 386 CYS Chi-restraints excluded: chain B residue 414 LEU 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 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 746 GLU Chi-restraints excluded: chain C residue 207 ILE 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 503 LEU Chi-restraints excluded: chain C residue 506 LEU 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: 0.9980 chunk 167 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 127 optimal weight: 0.0980 chunk 203 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3669 r_free = 0.3669 target = 0.127849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.097585 restraints weight = 38503.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.100543 restraints weight = 18577.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.102577 restraints weight = 11951.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.103780 restraints weight = 9075.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.104588 restraints weight = 7693.133| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18033 Z= 0.113 Angle : 0.586 11.520 24463 Z= 0.301 Chirality : 0.038 0.143 2752 Planarity : 0.003 0.045 3012 Dihedral : 4.594 55.237 2401 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.32 % Allowed : 18.67 % Favored : 79.01 % 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: 1.57 (0.19), residues: 2136 helix: 2.33 (0.14), residues: 1280 sheet: 0.16 (0.56), residues: 76 loop : -1.15 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 420 TYR 0.024 0.001 TYR A 666 PHE 0.023 0.001 PHE D 266 TRP 0.017 0.001 TRP B 372 HIS 0.016 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (18032) covalent geometry : angle 0.58614 / 0.30 (24463) hydrogen bonds : bond 0.03952 / 2.60 ( 1010) hydrogen bonds : angle 3.83411 / 2.74 ( 2907) Misc. bond : bond 0.00021 / 0.01 ( 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 556 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 512 time to evaluate : 0.616 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: 0.7701 (t80) cc_final: 0.6985 (t80) REVERT: A 308 MET cc_start: 0.9109 (mmm) cc_final: 0.8284 (mtp) REVERT: A 481 SER cc_start: 0.9612 (m) cc_final: 0.9171 (p) REVERT: A 562 MET cc_start: 0.8809 (mmm) cc_final: 0.8485 (mmm) REVERT: A 601 ASP cc_start: 0.7526 (t0) cc_final: 0.7179 (p0) REVERT: A 648 GLU cc_start: 0.8570 (tt0) cc_final: 0.8118 (pp20) REVERT: A 704 THR cc_start: 0.9282 (m) cc_final: 0.9033 (p) REVERT: A 737 ASP cc_start: 0.5883 (p0) cc_final: 0.5628 (p0) REVERT: D 211 ARG cc_start: 0.9305 (mmt180) cc_final: 0.8999 (mpt90) REVERT: D 253 SER cc_start: 0.9330 (m) cc_final: 0.8980 (p) REVERT: D 308 MET cc_start: 0.9185 (mmm) cc_final: 0.8898 (mmm) REVERT: D 351 TYR cc_start: 0.8970 (t80) cc_final: 0.8648 (t80) REVERT: D 369 PHE cc_start: 0.6865 (t80) cc_final: 0.6397 (t80) REVERT: D 383 ASP cc_start: 0.8241 (p0) cc_final: 0.7345 (t0) REVERT: D 384 LEU cc_start: 0.8605 (mt) cc_final: 0.8290 (mp) REVERT: D 406 THR cc_start: 0.8489 (m) cc_final: 0.8161 (p) REVERT: D 585 LEU cc_start: 0.9327 (mt) cc_final: 0.9117 (mm) REVERT: D 716 MET cc_start: 0.5808 (ttm) cc_final: 0.5519 (tpt) REVERT: B 214 MET cc_start: 0.9043 (pmm) cc_final: 0.8765 (pmm) REVERT: B 305 VAL cc_start: 0.9622 (t) cc_final: 0.9407 (p) REVERT: B 383 ASP cc_start: 0.8136 (t70) cc_final: 0.7890 (t70) REVERT: B 397 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8252 (mt-10) REVERT: B 491 ARG cc_start: 0.9030 (mmm-85) cc_final: 0.8786 (mmm-85) REVERT: B 649 PHE cc_start: 0.6074 (m-80) cc_final: 0.5550 (m-80) REVERT: C 228 GLN cc_start: 0.8471 (mt0) cc_final: 0.8193 (pm20) REVERT: C 246 TYR cc_start: 0.7020 (t80) cc_final: 0.6693 (t80) REVERT: C 308 MET cc_start: 0.9217 (mmm) cc_final: 0.8832 (mtp) REVERT: C 309 TYR cc_start: 0.9091 (t80) cc_final: 0.8708 (t80) REVERT: C 562 MET cc_start: 0.8928 (mmm) cc_final: 0.8293 (mmp) REVERT: C 700 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8481 (tp-100) outliers start: 44 outliers final: 30 residues processed: 529 average time/residue: 0.1140 time to fit residues: 94.7678 Evaluate side-chains 512 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 482 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 447 ILE Chi-restraints excluded: chain A residue 544 SER 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 686 VAL Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain B residue 414 LEU 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 686 VAL Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 ILE 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 637 LEU Chi-restraints excluded: chain C residue 660 ILE 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: 0.8980 chunk 80 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 201 optimal weight: 0.5980 chunk 161 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.127709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.097555 restraints weight = 38480.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.100462 restraints weight = 18652.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.102427 restraints weight = 12014.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.103686 restraints weight = 9170.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.104370 restraints weight = 7744.760| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4360 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= 0.121 Angle : 0.598 11.950 24463 Z= 0.302 Chirality : 0.039 0.203 2752 Planarity : 0.003 0.043 3012 Dihedral : 4.317 54.681 2397 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.06 % Allowed : 20.04 % Favored : 77.90 % 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: 1.54 (0.19), residues: 2136 helix: 2.30 (0.14), residues: 1280 sheet: 0.22 (0.58), residues: 76 loop : -1.15 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 420 TYR 0.022 0.001 TYR A 666 PHE 0.020 0.001 PHE D 266 TRP 0.024 0.001 TRP B 372 HIS 0.011 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (18032) covalent geometry : angle 0.59849 / 0.30 (24463) hydrogen bonds : bond 0.03955 / 2.59 ( 1010) hydrogen bonds : angle 3.86325 / 2.76 ( 2907) Misc. bond : bond 0.00029 / 0.02 ( 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 533 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 494 time to evaluate : 0.599 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: 0.7866 (t80) cc_final: 0.7392 (t80) REVERT: A 308 MET cc_start: 0.9098 (mmm) cc_final: 0.8676 (tpp) REVERT: A 481 SER cc_start: 0.9543 (m) cc_final: 0.9207 (p) REVERT: A 601 ASP cc_start: 0.7479 (t0) cc_final: 0.7169 (p0) REVERT: A 648 GLU cc_start: 0.8587 (tt0) cc_final: 0.8113 (pp20) REVERT: A 704 THR cc_start: 0.9283 (m) cc_final: 0.9041 (p) REVERT: A 737 ASP cc_start: 0.5749 (p0) cc_final: 0.5536 (p0) REVERT: D 211 ARG cc_start: 0.9295 (mmt180) cc_final: 0.8807 (mpt90) REVERT: D 253 SER cc_start: 0.9343 (m) cc_final: 0.9011 (p) REVERT: D 351 TYR cc_start: 0.8975 (t80) cc_final: 0.8662 (t80) REVERT: D 369 PHE cc_start: 0.6829 (t80) cc_final: 0.6323 (t80) REVERT: D 383 ASP cc_start: 0.8245 (p0) cc_final: 0.7281 (t0) REVERT: D 384 LEU cc_start: 0.8626 (mt) cc_final: 0.8337 (mp) REVERT: D 406 THR cc_start: 0.8431 (m) cc_final: 0.8127 (p) REVERT: D 716 MET cc_start: 0.5803 (ttm) cc_final: 0.5588 (tpt) REVERT: D 746 GLU cc_start: 0.6248 (OUTLIER) cc_final: 0.5769 (pm20) REVERT: B 214 MET cc_start: 0.9055 (pmm) cc_final: 0.8758 (pmm) REVERT: B 305 VAL cc_start: 0.9616 (t) cc_final: 0.9389 (p) REVERT: B 383 ASP cc_start: 0.8118 (t70) cc_final: 0.7871 (t70) REVERT: B 397 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8291 (mt-10) REVERT: B 491 ARG cc_start: 0.9014 (mmm-85) cc_final: 0.8749 (mmm-85) REVERT: B 656 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8371 (tttp) REVERT: C 228 GLN cc_start: 0.8443 (mt0) cc_final: 0.8195 (pm20) REVERT: C 246 TYR cc_start: 0.7122 (t80) cc_final: 0.6799 (t80) REVERT: C 397 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8145 (mt-10) REVERT: C 562 MET cc_start: 0.8916 (mmm) cc_final: 0.8214 (mmp) REVERT: C 700 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8442 (tp-100) outliers start: 39 outliers final: 30 residues processed: 513 average time/residue: 0.1121 time to fit residues: 89.8379 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 : 0.685 ------------------------------------------------------------------------------- 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 447 ILE Chi-restraints excluded: chain A residue 544 SER 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 686 VAL Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain D residue 746 GLU Chi-restraints excluded: chain B residue 414 LEU 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 656 LYS Chi-restraints excluded: chain B residue 746 GLU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 215 THR 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 637 LEU Chi-restraints excluded: chain C residue 660 ILE 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: 4.9990 chunk 11 optimal weight: 8.9990 chunk 132 optimal weight: 0.0970 chunk 172 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 378 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 = 0.3613 r_free = 0.3613 target = 0.123810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.093558 restraints weight = 39088.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.096338 restraints weight = 19273.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098230 restraints weight = 12553.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.099388 restraints weight = 9614.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.099992 restraints weight = 8176.414| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 18033 Z= 0.230 Angle : 0.694 12.416 24463 Z= 0.349 Chirality : 0.042 0.251 2752 Planarity : 0.004 0.044 3012 Dihedral : 4.491 47.792 2397 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.80 % Allowed : 20.25 % 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: 1.30 (0.19), residues: 2136 helix: 2.11 (0.14), residues: 1292 sheet: 0.06 (0.57), residues: 76 loop : -1.30 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 420 TYR 0.022 0.002 TYR D 666 PHE 0.018 0.001 PHE D 580 TRP 0.029 0.002 TRP B 372 HIS 0.009 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 (18032) covalent geometry : angle 0.69445 / 0.35 (24463) hydrogen bonds : bond 0.04696 / 3.05 ( 1010) hydrogen bonds : angle 4.10853 / 2.91 ( 2907) Misc. bond : bond 0.00088 / 0.05 ( 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 526 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 473 time to evaluate : 0.632 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: A 304 PHE cc_start: 0.7785 (t80) cc_final: 0.7199 (t80) REVERT: A 308 MET cc_start: 0.9120 (mmm) cc_final: 0.8689 (tpp) REVERT: A 309 TYR cc_start: 0.9117 (t80) cc_final: 0.8792 (t80) REVERT: A 313 LEU cc_start: 0.9493 (mt) cc_final: 0.9234 (mt) REVERT: A 481 SER cc_start: 0.9636 (m) cc_final: 0.9220 (p) REVERT: A 601 ASP cc_start: 0.7576 (t0) cc_final: 0.7115 (p0) REVERT: A 648 GLU cc_start: 0.8592 (tt0) cc_final: 0.8120 (pp20) REVERT: A 704 THR cc_start: 0.9352 (m) cc_final: 0.9150 (p) REVERT: A 737 ASP cc_start: 0.5858 (p0) cc_final: 0.5630 (p0) REVERT: D 253 SER cc_start: 0.9348 (m) cc_final: 0.9065 (p) REVERT: D 383 ASP cc_start: 0.8122 (p0) cc_final: 0.7291 (t0) REVERT: D 384 LEU cc_start: 0.8653 (mt) cc_final: 0.8311 (mp) REVERT: D 406 THR cc_start: 0.8485 (m) cc_final: 0.8205 (p) REVERT: D 581 MET cc_start: 0.7027 (tpp) cc_final: 0.6758 (tpp) REVERT: D 585 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8865 (mm) REVERT: D 716 MET cc_start: 0.5994 (ttm) cc_final: 0.5725 (tpt) REVERT: D 746 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.5842 (pm20) REVERT: B 214 MET cc_start: 0.9043 (pmm) cc_final: 0.8742 (pmm) REVERT: B 383 ASP cc_start: 0.8252 (t70) cc_final: 0.8009 (t70) REVERT: B 397 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8293 (mt-10) REVERT: B 562 MET cc_start: 0.7966 (tpp) cc_final: 0.7763 (tpp) REVERT: B 656 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8391 (tttp) REVERT: B 716 MET cc_start: 0.5947 (tmm) cc_final: 0.5728 (tpp) REVERT: C 228 GLN cc_start: 0.8407 (mt0) cc_final: 0.8118 (pm20) REVERT: C 246 TYR cc_start: 0.7253 (t80) cc_final: 0.6911 (t80) REVERT: C 700 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8530 (tp-100) outliers start: 53 outliers final: 37 residues processed: 499 average time/residue: 0.1177 time to fit residues: 91.4394 Evaluate side-chains 504 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 464 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 520 SER Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 632 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 585 LEU Chi-restraints excluded: chain D residue 635 LEU 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 D residue 746 GLU Chi-restraints excluded: chain B residue 219 LEU 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 656 LYS Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 320 HIS 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 637 LEU Chi-restraints excluded: chain C residue 660 ILE 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: 0.0870 chunk 116 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 69 optimal weight: 0.3980 chunk 84 optimal weight: 0.0670 chunk 145 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 259 ASN ** D 378 HIS ** 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 = 0.3663 r_free = 0.3663 target = 0.127669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.097551 restraints weight = 38246.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.100451 restraints weight = 18433.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.102454 restraints weight = 11965.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103677 restraints weight = 9143.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.104345 restraints weight = 7741.850| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18033 Z= 0.122 Angle : 0.661 13.492 24463 Z= 0.328 Chirality : 0.040 0.364 2752 Planarity : 0.003 0.043 3012 Dihedral : 4.387 59.978 2397 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.48 % Allowed : 22.05 % Favored : 76.48 % 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: 1.45 (0.19), residues: 2136 helix: 2.22 (0.14), residues: 1280 sheet: 0.25 (0.60), residues: 76 loop : -1.19 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 491 TYR 0.023 0.001 TYR A 309 PHE 0.029 0.001 PHE A 712 TRP 0.026 0.001 TRP B 372 HIS 0.012 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (18032) covalent geometry : angle 0.66142 / 0.33 (24463) hydrogen bonds : bond 0.04091 / 2.69 ( 1010) hydrogen bonds : angle 3.97151 / 2.84 ( 2907) Misc. bond : bond 0.00025 / 0.01 ( 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 524 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 496 time to evaluate : 0.554 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: 0.7811 (t80) cc_final: 0.7399 (t80) REVERT: A 308 MET cc_start: 0.9070 (mmm) cc_final: 0.8672 (tpp) REVERT: A 481 SER cc_start: 0.9612 (m) cc_final: 0.9195 (p) REVERT: A 601 ASP cc_start: 0.7493 (t0) cc_final: 0.7158 (p0) REVERT: A 648 GLU cc_start: 0.8593 (tt0) cc_final: 0.8130 (pp20) REVERT: A 704 THR cc_start: 0.9282 (m) cc_final: 0.9049 (p) REVERT: A 737 ASP cc_start: 0.5704 (p0) cc_final: 0.2794 (p0) REVERT: D 211 ARG cc_start: 0.9299 (mmt180) cc_final: 0.8815 (mpt90) REVERT: D 253 SER cc_start: 0.9354 (m) cc_final: 0.9025 (p) REVERT: D 351 TYR cc_start: 0.9019 (t80) cc_final: 0.8733 (t80) REVERT: D 383 ASP cc_start: 0.8235 (p0) cc_final: 0.7197 (t0) REVERT: D 384 LEU cc_start: 0.8676 (mt) cc_final: 0.8380 (mp) REVERT: D 406 THR cc_start: 0.8456 (m) cc_final: 0.8197 (p) REVERT: D 666 TYR cc_start: 0.8773 (t80) cc_final: 0.8524 (t80) REVERT: D 746 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.5905 (pm20) REVERT: B 214 MET cc_start: 0.9032 (pmm) cc_final: 0.8730 (pmm) REVERT: B 383 ASP cc_start: 0.8150 (t70) cc_final: 0.7928 (t70) REVERT: B 423 GLN cc_start: 0.8694 (tp40) cc_final: 0.8279 (tp-100) REVERT: B 716 MET cc_start: 0.5953 (tmm) cc_final: 0.5737 (tpp) REVERT: C 228 GLN cc_start: 0.8433 (mt0) cc_final: 0.8166 (pm20) REVERT: C 246 TYR cc_start: 0.7204 (t80) cc_final: 0.6869 (t80) REVERT: C 261 LEU cc_start: 0.8906 (pt) cc_final: 0.8129 (tp) REVERT: C 309 TYR cc_start: 0.9047 (t80) cc_final: 0.8698 (t80) REVERT: C 383 ASP cc_start: 0.8087 (t70) cc_final: 0.7733 (t0) REVERT: C 397 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8130 (mt-10) REVERT: C 700 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8472 (tp-100) outliers start: 28 outliers final: 24 residues processed: 511 average time/residue: 0.1225 time to fit residues: 97.5995 Evaluate side-chains 505 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 480 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 497 LEU 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 378 HIS Chi-restraints excluded: chain D residue 437 ASN Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 697 TRP Chi-restraints excluded: chain D residue 746 GLU 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 592 SER Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 207 ILE 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 660 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 171 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 147 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 378 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 = 0.3654 r_free = 0.3654 target = 0.126926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.097002 restraints weight = 38932.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.099922 restraints weight = 18773.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.101901 restraints weight = 12093.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.102902 restraints weight = 9192.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.103790 restraints weight = 7882.924| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18033 Z= 0.129 Angle : 0.666 13.968 24463 Z= 0.331 Chirality : 0.040 0.436 2752 Planarity : 0.004 0.045 3012 Dihedral : 4.341 57.840 2397 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.74 % Allowed : 22.05 % Favored : 76.21 % 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: 1.40 (0.19), residues: 2136 helix: 2.17 (0.14), residues: 1280 sheet: 0.31 (0.61), residues: 76 loop : -1.20 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 491 TYR 0.021 0.001 TYR A 738 PHE 0.021 0.001 PHE A 712 TRP 0.026 0.001 TRP B 372 HIS 0.011 0.001 HIS D 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (18032) covalent geometry : angle 0.66627 / 0.33 (24463) hydrogen bonds : bond 0.04107 / 2.68 ( 1010) hydrogen bonds : angle 4.03564 / 2.89 ( 2907) Misc. bond : bond 0.00025 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3138.27 seconds wall clock time: 54 minutes 57.97 seconds (3297.97 seconds total)