Starting phenix.real_space_refine on Sat Aug 23 18:33:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ztr_60470/08_2025/8ztr_60470.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ztr_60470/08_2025/8ztr_60470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ztr_60470/08_2025/8ztr_60470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ztr_60470/08_2025/8ztr_60470.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ztr_60470/08_2025/8ztr_60470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ztr_60470/08_2025/8ztr_60470.map" } resolution = 3.26 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= 0.002 sd= 0.030 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 9088 2.51 5 N 2254 2.21 5 O 2676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14072 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5887 Classifications: {'peptide': 702} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 692} Chain: "B" Number of atoms: 5887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5887 Classifications: {'peptide': 702} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 692} Chain: "E" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1149 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain breaks: 1 Chain: "F" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1149 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain breaks: 1 Time building chain proxies: 2.97, per 1000 atoms: 0.21 Number of scatterers: 14072 At special positions: 0 Unit cell: (130.48, 100.656, 108.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2676 8.00 N 2254 7.00 C 9088 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=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 537.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3232 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 6 sheets defined 63.8% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 304 through 317 removed outlier: 3.543A pdb=" N VAL A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 321 removed outlier: 3.752A pdb=" N ALA A 321 " --> pdb=" O PRO A 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 327 through 334 removed outlier: 3.529A pdb=" N HIS A 332 " --> pdb=" O ASP A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 366 Processing helix chain 'A' and resid 366 through 373 removed outlier: 3.622A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 392 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'A' and resid 447 through 466 Processing helix chain 'A' and resid 467 through 501 removed outlier: 5.424A pdb=" N LEU A 497 " --> pdb=" O ASN A 493 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU A 498 " --> pdb=" O GLY A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 removed outlier: 3.742A pdb=" N MET A 519 " --> pdb=" O ILE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 527 removed outlier: 3.558A pdb=" N ASP A 526 " --> pdb=" O ASN A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 546 removed outlier: 4.232A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 572 removed outlier: 3.772A pdb=" N VAL A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 598 removed outlier: 3.598A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.799A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 629 Processing helix chain 'A' and resid 632 through 639 Processing helix chain 'A' and resid 648 through 659 Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 680 through 701 removed outlier: 3.733A pdb=" N ALA A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 723 removed outlier: 4.237A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 743 Processing helix chain 'A' and resid 750 through 764 removed outlier: 4.267A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 removed outlier: 3.582A pdb=" N ILE A 772 " --> pdb=" O PRO A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.622A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 827 removed outlier: 3.857A pdb=" N LEU A 825 " --> pdb=" O SER A 821 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS A 826 " --> pdb=" O GLU A 822 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 827 " --> pdb=" O ILE A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 841 removed outlier: 3.523A pdb=" N ILE A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 857 Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 878 through 900 Processing helix chain 'A' and resid 908 through 922 removed outlier: 3.638A pdb=" N TYR A 912 " --> pdb=" O SER A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 933 removed outlier: 3.641A pdb=" N MET A 930 " --> pdb=" O ASN A 927 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU A 931 " --> pdb=" O SER A 928 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 933 " --> pdb=" O MET A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 955 through 961 Processing helix chain 'A' and resid 963 through 973 Processing helix chain 'A' and resid 973 through 991 removed outlier: 4.399A pdb=" N HIS A 979 " --> pdb=" O HIS A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1003 Processing helix chain 'B' and resid 305 through 317 Processing helix chain 'B' and resid 318 through 321 removed outlier: 3.608A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 318 through 321' Processing helix chain 'B' and resid 327 through 333 Processing helix chain 'B' and resid 355 through 366 Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.525A pdb=" N ARG B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 392 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 466 removed outlier: 4.389A pdb=" N ASP B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 500 removed outlier: 4.962A pdb=" N LEU B 497 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU B 498 " --> pdb=" O GLY B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 removed outlier: 4.176A pdb=" N MET B 519 " --> pdb=" O ILE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 3.568A pdb=" N ASP B 526 " --> pdb=" O ASN B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 542 through 547 removed outlier: 3.889A pdb=" N SER B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 542 through 547' Processing helix chain 'B' and resid 552 through 572 Processing helix chain 'B' and resid 579 through 598 Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.529A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 628 removed outlier: 3.800A pdb=" N THR B 628 " --> pdb=" O GLU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 639 removed outlier: 4.023A pdb=" N PHE B 639 " --> pdb=" O GLY B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 659 Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 680 through 701 removed outlier: 3.658A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 723 removed outlier: 4.426A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 743 Processing helix chain 'B' and resid 750 through 762 Processing helix chain 'B' and resid 768 through 786 removed outlier: 3.561A pdb=" N ILE B 772 " --> pdb=" O PRO B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 812 removed outlier: 3.627A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 826 removed outlier: 3.605A pdb=" N CYS B 826 " --> pdb=" O GLU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 841 removed outlier: 4.072A pdb=" N LYS B 840 " --> pdb=" O ASP B 836 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU B 841 " --> pdb=" O PHE B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 857 Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 878 through 903 removed outlier: 4.699A pdb=" N GLU B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS B 902 " --> pdb=" O VAL B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 922 Processing helix chain 'B' and resid 927 through 934 removed outlier: 3.519A pdb=" N GLU B 931 " --> pdb=" O SER B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 945 removed outlier: 4.035A pdb=" N PHE B 943 " --> pdb=" O GLN B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 954 Processing helix chain 'B' and resid 955 through 960 Processing helix chain 'B' and resid 963 through 972 Processing helix chain 'B' and resid 976 through 991 removed outlier: 3.598A pdb=" N VAL B 980 " --> pdb=" O MET B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1003 removed outlier: 3.697A pdb=" N LEU B 997 " --> pdb=" O ASP B 993 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 76 removed outlier: 3.723A pdb=" N THR E 76 " --> pdb=" O TRP E 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 76 removed outlier: 3.737A pdb=" N THR F 76 " --> pdb=" O TRP F 72 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA2, first strand: chain 'A' and resid 574 through 575 removed outlier: 6.766A pdb=" N PHE F 13 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR F 24 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL F 11 " --> pdb=" O THR F 24 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR F 171 " --> pdb=" O ASN F 197 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN F 197 " --> pdb=" O TYR F 171 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE F 193 " --> pdb=" O TYR F 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 575 removed outlier: 8.409A pdb=" N VAL F 22 " --> pdb=" O PHE F 68 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N PHE F 68 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR F 24 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA F 66 " --> pdb=" O THR F 24 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N THR F 62 " --> pdb=" O GLN F 28 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ALA F 30 " --> pdb=" O ASN F 60 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN F 60 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N PHE F 32 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLU F 58 " --> pdb=" O PHE F 32 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLN F 34 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N GLU F 56 " --> pdb=" O GLN F 34 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE F 59 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU F 61 " --> pdb=" O PHE F 220 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AA5, first strand: chain 'B' and resid 574 through 575 removed outlier: 4.470A pdb=" N GLU E 26 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASN E 65 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N GLN E 28 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL E 63 " --> pdb=" O GLN E 28 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA E 30 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU E 61 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N PHE E 32 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE E 59 " --> pdb=" O PHE E 32 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLN E 34 " --> pdb=" O LYS E 57 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LYS E 57 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU E 61 " --> pdb=" O PHE E 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 574 through 575 removed outlier: 6.698A pdb=" N PHE E 13 " --> pdb=" O VAL E 22 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR E 24 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL E 11 " --> pdb=" O THR E 24 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N TYR E 171 " --> pdb=" O ASN E 197 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN E 197 " --> pdb=" O TYR E 171 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN E 194 " --> pdb=" O VAL E 233 " (cutoff:3.500A) 763 hydrogen bonds defined for protein. 2172 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.83 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2391 1.31 - 1.44: 3992 1.44 - 1.56: 7907 1.56 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 14382 Sorted by residual: bond pdb=" C ASN A 598 " pdb=" O ASN A 598 " ideal model delta sigma weight residual 1.236 1.184 0.052 1.32e-02 5.74e+03 1.53e+01 bond pdb=" C ASN A 910 " pdb=" O ASN A 910 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.26e-02 6.30e+03 1.41e+01 bond pdb=" C ASP A 911 " pdb=" O ASP A 911 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.15e-02 7.56e+03 1.11e+01 bond pdb=" C ARG A 447 " pdb=" O ARG A 447 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.26e-02 6.30e+03 9.69e+00 bond pdb=" CA ASP A 788 " pdb=" C ASP A 788 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.32e-02 5.74e+03 8.07e+00 ... (remaining 14377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 18994 2.51 - 5.02: 313 5.02 - 7.53: 32 7.53 - 10.04: 8 10.04 - 12.55: 3 Bond angle restraints: 19350 Sorted by residual: angle pdb=" N LYS B 660 " pdb=" CA LYS B 660 " pdb=" C LYS B 660 " ideal model delta sigma weight residual 110.46 97.91 12.55 1.48e+00 4.57e-01 7.19e+01 angle pdb=" N PHE B 744 " pdb=" CA PHE B 744 " pdb=" C PHE B 744 " ideal model delta sigma weight residual 109.83 100.76 9.07 1.27e+00 6.20e-01 5.10e+01 angle pdb=" N ARG A 447 " pdb=" CA ARG A 447 " pdb=" C ARG A 447 " ideal model delta sigma weight residual 110.80 99.05 11.75 2.13e+00 2.20e-01 3.04e+01 angle pdb=" C ASN F 210 " pdb=" CA ASN F 210 " pdb=" CB ASN F 210 " ideal model delta sigma weight residual 110.08 101.63 8.45 1.57e+00 4.06e-01 2.90e+01 angle pdb=" N ASN A 702 " pdb=" CA ASN A 702 " pdb=" C ASN A 702 " ideal model delta sigma weight residual 111.28 105.89 5.39 1.09e+00 8.42e-01 2.45e+01 ... (remaining 19345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7329 17.98 - 35.96: 947 35.96 - 53.95: 253 53.95 - 71.93: 46 71.93 - 89.91: 21 Dihedral angle restraints: 8596 sinusoidal: 3574 harmonic: 5022 Sorted by residual: dihedral pdb=" C ASN F 210 " pdb=" N ASN F 210 " pdb=" CA ASN F 210 " pdb=" CB ASN F 210 " ideal model delta harmonic sigma weight residual -122.60 -112.10 -10.50 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" CA GLU F 230 " pdb=" C GLU F 230 " pdb=" N MET F 231 " pdb=" CA MET F 231 " ideal model delta harmonic sigma weight residual -180.00 -161.79 -18.21 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA THR E 8 " pdb=" C THR E 8 " pdb=" N ALA E 9 " pdb=" CA ALA E 9 " ideal model delta harmonic sigma weight residual 180.00 -162.09 -17.91 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 8593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1618 0.046 - 0.093: 333 0.093 - 0.139: 84 0.139 - 0.186: 13 0.186 - 0.232: 4 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CA TYR B1003 " pdb=" N TYR B1003 " pdb=" C TYR B1003 " pdb=" CB TYR B1003 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PHE A 907 " pdb=" N PHE A 907 " pdb=" C PHE A 907 " pdb=" CB PHE A 907 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ASN A 963 " pdb=" N ASN A 963 " pdb=" C ASN A 963 " pdb=" CB ASN A 963 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.62e-01 ... (remaining 2049 not shown) Planarity restraints: 2480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B1003 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C TYR B1003 " 0.062 2.00e-02 2.50e+03 pdb=" O TYR B1003 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE B1004 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 195 " -0.056 5.00e-02 4.00e+02 8.50e-02 1.16e+01 pdb=" N PRO E 196 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO E 196 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO E 196 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 409 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C ILE B 409 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE B 409 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN B 410 " -0.015 2.00e-02 2.50e+03 ... (remaining 2477 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1099 2.74 - 3.28: 15609 3.28 - 3.82: 24104 3.82 - 4.36: 28760 4.36 - 4.90: 48426 Nonbonded interactions: 117998 Sorted by model distance: nonbonded pdb=" O LEU A 551 " pdb=" OG1 THR A 555 " model vdw 2.195 3.040 nonbonded pdb=" O LYS B 785 " pdb=" NZ LYS B 785 " model vdw 2.207 3.120 nonbonded pdb=" OE2 GLU E 174 " pdb=" NH2 ARG E 176 " model vdw 2.230 3.120 nonbonded pdb=" O PHE A 559 " pdb=" OG1 THR A 562 " model vdw 2.236 3.040 nonbonded pdb=" O SER A 573 " pdb=" NH2 ARG A 629 " model vdw 2.237 3.120 ... (remaining 117993 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.920 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5810 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 : 0.005 0.055 14382 Z= 0.260 Angle : 0.806 12.553 19350 Z= 0.476 Chirality : 0.043 0.232 2052 Planarity : 0.005 0.085 2480 Dihedral : 17.600 89.912 5364 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.76 % Favored : 95.18 % Rotamer: Outliers : 0.45 % Allowed : 19.66 % Favored : 79.88 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.20), residues: 1682 helix: 0.48 (0.16), residues: 963 sheet: -1.83 (0.44), residues: 112 loop : -1.76 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 447 TYR 0.038 0.002 TYR B1003 PHE 0.041 0.002 PHE F 32 TRP 0.008 0.001 TRP B 958 HIS 0.004 0.001 HIS A 786 Details of bonding type rmsd covalent geometry : bond 0.00452 (14382) covalent geometry : angle 0.80613 (19350) hydrogen bonds : bond 0.15205 ( 755) hydrogen bonds : angle 6.16594 ( 2172) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 218 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 MET cc_start: 0.8397 (mmm) cc_final: 0.7900 (mmt) REVERT: A 950 ASP cc_start: 0.6581 (p0) cc_final: 0.6358 (p0) REVERT: B 406 SER cc_start: 0.6640 (t) cc_final: 0.6268 (m) REVERT: B 607 GLU cc_start: 0.6734 (mp0) cc_final: 0.6529 (mp0) REVERT: B 693 GLU cc_start: 0.6235 (mp0) cc_final: 0.5351 (mm-30) REVERT: F 219 LYS cc_start: 0.8026 (mtpp) cc_final: 0.7631 (mtpp) outliers start: 7 outliers final: 1 residues processed: 224 average time/residue: 0.0947 time to fit residues: 31.6087 Evaluate side-chains 189 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 233 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 503 HIS A 614 ASN A 797 ASN B 591 ASN B 609 HIS ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 HIS B 895 ASN B 961 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.248138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.214928 restraints weight = 17137.829| |-----------------------------------------------------------------------------| r_work (start): 0.4481 rms_B_bonded: 2.20 r_work: 0.4341 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14382 Z= 0.154 Angle : 0.600 12.233 19350 Z= 0.318 Chirality : 0.042 0.354 2052 Planarity : 0.004 0.078 2480 Dihedral : 4.568 34.003 1859 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.04 % Allowed : 20.57 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.20), residues: 1682 helix: 0.78 (0.16), residues: 965 sheet: -1.65 (0.46), residues: 100 loop : -1.58 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 380 TYR 0.016 0.002 TYR B 804 PHE 0.017 0.002 PHE A 708 TRP 0.016 0.002 TRP A 958 HIS 0.007 0.001 HIS B 852 Details of bonding type rmsd covalent geometry : bond 0.00352 (14382) covalent geometry : angle 0.59979 (19350) hydrogen bonds : bond 0.04162 ( 755) hydrogen bonds : angle 4.92059 ( 2172) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 226 time to evaluate : 0.388 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 306 ASP cc_start: 0.5380 (OUTLIER) cc_final: 0.5019 (t0) REVERT: A 381 PHE cc_start: 0.8071 (t80) cc_final: 0.7778 (t80) REVERT: A 616 MET cc_start: 0.8412 (mmm) cc_final: 0.8135 (mmm) REVERT: A 626 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7648 (mm-30) REVERT: A 663 ASP cc_start: 0.5744 (m-30) cc_final: 0.5419 (m-30) REVERT: A 738 LYS cc_start: 0.7469 (mmtt) cc_final: 0.7227 (mmtt) REVERT: A 950 ASP cc_start: 0.6948 (p0) cc_final: 0.6640 (p0) REVERT: B 331 LYS cc_start: 0.7529 (ptpt) cc_final: 0.7291 (pttp) REVERT: B 406 SER cc_start: 0.6473 (t) cc_final: 0.6238 (m) REVERT: B 544 PHE cc_start: 0.6400 (t80) cc_final: 0.6092 (t80) REVERT: B 552 TYR cc_start: 0.6230 (OUTLIER) cc_final: 0.5508 (t80) REVERT: B 562 THR cc_start: 0.7760 (m) cc_final: 0.7519 (p) REVERT: B 578 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7506 (ttp) REVERT: B 857 LYS cc_start: 0.5279 (tttt) cc_final: 0.4449 (ttmt) REVERT: B 964 ASP cc_start: 0.5127 (m-30) cc_final: 0.4925 (t70) outliers start: 47 outliers final: 23 residues processed: 255 average time/residue: 0.1057 time to fit residues: 39.3734 Evaluate side-chains 222 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 552 TYR Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain F residue 67 PHE Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 235 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 118 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 108 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 HIS A 477 ASN A 503 HIS B 475 GLN B 483 GLN B 563 ASN B 698 GLN B 852 HIS B 961 ASN E 210 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.246513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.213559 restraints weight = 17262.397| |-----------------------------------------------------------------------------| r_work (start): 0.4467 rms_B_bonded: 2.17 r_work: 0.4332 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14382 Z= 0.140 Angle : 0.570 11.746 19350 Z= 0.302 Chirality : 0.041 0.281 2052 Planarity : 0.004 0.072 2480 Dihedral : 4.439 29.916 1858 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.36 % Allowed : 21.15 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.20), residues: 1682 helix: 0.82 (0.16), residues: 966 sheet: -1.46 (0.47), residues: 100 loop : -1.64 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 176 TYR 0.020 0.002 TYR A 625 PHE 0.024 0.001 PHE A 387 TRP 0.014 0.001 TRP A 958 HIS 0.007 0.001 HIS B 852 Details of bonding type rmsd covalent geometry : bond 0.00318 (14382) covalent geometry : angle 0.56962 (19350) hydrogen bonds : bond 0.03775 ( 755) hydrogen bonds : angle 4.73126 ( 2172) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 214 time to evaluate : 0.523 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 306 ASP cc_start: 0.5319 (OUTLIER) cc_final: 0.4957 (t0) REVERT: A 364 LYS cc_start: 0.7621 (tttt) cc_final: 0.6635 (ttmt) REVERT: A 387 PHE cc_start: 0.6265 (t80) cc_final: 0.6049 (t80) REVERT: A 503 HIS cc_start: 0.7424 (OUTLIER) cc_final: 0.7022 (p-80) REVERT: A 616 MET cc_start: 0.8432 (mmm) cc_final: 0.8187 (mmm) REVERT: A 626 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7628 (mm-30) REVERT: A 738 LYS cc_start: 0.7495 (mmtt) cc_final: 0.7225 (mmtt) REVERT: A 802 ARG cc_start: 0.6053 (ptt180) cc_final: 0.5069 (ptp90) REVERT: A 950 ASP cc_start: 0.6938 (p0) cc_final: 0.6599 (p0) REVERT: A 1001 MET cc_start: 0.5954 (mmm) cc_final: 0.5551 (mmm) REVERT: B 331 LYS cc_start: 0.7594 (ptpt) cc_final: 0.7337 (pttp) REVERT: B 552 TYR cc_start: 0.6079 (OUTLIER) cc_final: 0.4769 (t80) REVERT: B 562 THR cc_start: 0.7720 (m) cc_final: 0.7419 (p) REVERT: B 765 ASN cc_start: 0.4664 (OUTLIER) cc_final: 0.1424 (t0) REVERT: B 976 MET cc_start: 0.6177 (tmm) cc_final: 0.5735 (tmm) REVERT: E 206 MET cc_start: 0.5376 (mmm) cc_final: 0.4790 (mtp) REVERT: E 231 MET cc_start: 0.1256 (ttt) cc_final: 0.0798 (mtt) REVERT: E 235 ILE cc_start: 0.5403 (OUTLIER) cc_final: 0.5054 (pp) REVERT: F 75 MET cc_start: 0.7009 (ptm) cc_final: 0.6671 (ptt) REVERT: F 176 ARG cc_start: 0.4952 (tmm160) cc_final: 0.4669 (ttp80) outliers start: 52 outliers final: 24 residues processed: 249 average time/residue: 0.1165 time to fit residues: 43.0705 Evaluate side-chains 232 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 552 TYR Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain F residue 67 PHE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 235 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 86 optimal weight: 0.0030 chunk 83 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 163 optimal weight: 0.5980 chunk 164 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 HIS B 475 GLN B 852 HIS ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.249759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.216574 restraints weight = 17370.434| |-----------------------------------------------------------------------------| r_work (start): 0.4481 rms_B_bonded: 2.22 r_work: 0.4344 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5905 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14382 Z= 0.121 Angle : 0.537 9.165 19350 Z= 0.289 Chirality : 0.040 0.184 2052 Planarity : 0.003 0.064 2480 Dihedral : 4.349 28.120 1858 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.17 % Allowed : 21.93 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.20), residues: 1682 helix: 0.89 (0.17), residues: 966 sheet: -1.46 (0.45), residues: 100 loop : -1.67 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 870 TYR 0.033 0.001 TYR A 625 PHE 0.019 0.001 PHE A 387 TRP 0.008 0.001 TRP A 958 HIS 0.008 0.001 HIS B 852 Details of bonding type rmsd covalent geometry : bond 0.00274 (14382) covalent geometry : angle 0.53687 (19350) hydrogen bonds : bond 0.03528 ( 755) hydrogen bonds : angle 4.63193 ( 2172) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 209 time to evaluate : 0.447 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 306 ASP cc_start: 0.5352 (OUTLIER) cc_final: 0.4999 (t0) REVERT: A 364 LYS cc_start: 0.7618 (tttt) cc_final: 0.6664 (ttmt) REVERT: A 389 GLU cc_start: 0.7006 (pp20) cc_final: 0.6747 (pp20) REVERT: A 503 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.6849 (p-80) REVERT: A 616 MET cc_start: 0.8376 (mmm) cc_final: 0.8131 (mmm) REVERT: A 626 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7659 (mm-30) REVERT: A 647 MET cc_start: 0.6808 (tpt) cc_final: 0.5070 (tpt) REVERT: A 687 TYR cc_start: 0.7126 (OUTLIER) cc_final: 0.5651 (t80) REVERT: A 807 LEU cc_start: 0.5586 (OUTLIER) cc_final: 0.5184 (tp) REVERT: A 950 ASP cc_start: 0.6934 (p0) cc_final: 0.6611 (p0) REVERT: A 1001 MET cc_start: 0.5891 (mmm) cc_final: 0.5558 (mmm) REVERT: B 331 LYS cc_start: 0.7546 (ptpt) cc_final: 0.7318 (pttp) REVERT: B 552 TYR cc_start: 0.6014 (OUTLIER) cc_final: 0.4817 (t80) REVERT: B 562 THR cc_start: 0.7712 (m) cc_final: 0.7423 (p) REVERT: B 763 LYS cc_start: 0.6656 (mptt) cc_final: 0.6346 (mptt) REVERT: B 765 ASN cc_start: 0.4688 (OUTLIER) cc_final: 0.1420 (t0) REVERT: B 976 MET cc_start: 0.6277 (tmm) cc_final: 0.4903 (mmt) REVERT: E 231 MET cc_start: 0.1166 (ttt) cc_final: 0.0662 (mtt) REVERT: F 75 MET cc_start: 0.6902 (ptm) cc_final: 0.6557 (ptt) outliers start: 49 outliers final: 30 residues processed: 243 average time/residue: 0.1133 time to fit residues: 41.3522 Evaluate side-chains 236 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 957 SER Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 552 TYR Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain F residue 67 PHE Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 235 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 132 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 141 optimal weight: 0.3980 chunk 96 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 135 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN A 503 HIS B 852 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.245913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.211775 restraints weight = 17113.002| |-----------------------------------------------------------------------------| r_work (start): 0.4478 rms_B_bonded: 2.24 r_work: 0.4337 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5911 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14382 Z= 0.119 Angle : 0.525 7.606 19350 Z= 0.283 Chirality : 0.039 0.248 2052 Planarity : 0.003 0.059 2480 Dihedral : 4.296 27.685 1858 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.56 % Allowed : 22.32 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.20), residues: 1682 helix: 0.92 (0.17), residues: 967 sheet: -1.25 (0.46), residues: 100 loop : -1.63 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 870 TYR 0.043 0.001 TYR A 625 PHE 0.028 0.001 PHE B 712 TRP 0.006 0.001 TRP A 958 HIS 0.009 0.001 HIS B 852 Details of bonding type rmsd covalent geometry : bond 0.00269 (14382) covalent geometry : angle 0.52470 (19350) hydrogen bonds : bond 0.03429 ( 755) hydrogen bonds : angle 4.56159 ( 2172) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 206 time to evaluate : 0.610 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: A 306 ASP cc_start: 0.5311 (OUTLIER) cc_final: 0.4980 (t0) REVERT: A 364 LYS cc_start: 0.7667 (tttt) cc_final: 0.6717 (ttmt) REVERT: A 389 GLU cc_start: 0.6973 (pp20) cc_final: 0.6685 (pp20) REVERT: A 503 HIS cc_start: 0.7677 (OUTLIER) cc_final: 0.6551 (p-80) REVERT: A 616 MET cc_start: 0.8421 (mmm) cc_final: 0.8189 (mmm) REVERT: A 626 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7647 (mm-30) REVERT: A 647 MET cc_start: 0.6907 (tpt) cc_final: 0.5137 (tpt) REVERT: A 687 TYR cc_start: 0.7070 (OUTLIER) cc_final: 0.5540 (t80) REVERT: A 807 LEU cc_start: 0.5602 (OUTLIER) cc_final: 0.5222 (tp) REVERT: A 950 ASP cc_start: 0.7018 (p0) cc_final: 0.6664 (p0) REVERT: A 1001 MET cc_start: 0.5951 (mmm) cc_final: 0.5652 (mmm) REVERT: B 331 LYS cc_start: 0.7524 (ptpt) cc_final: 0.7266 (pttp) REVERT: B 552 TYR cc_start: 0.6148 (OUTLIER) cc_final: 0.5035 (t80) REVERT: B 562 THR cc_start: 0.7717 (m) cc_final: 0.7409 (p) REVERT: B 624 GLU cc_start: 0.5860 (tp30) cc_final: 0.5599 (tp30) REVERT: B 711 GLN cc_start: 0.6369 (tm-30) cc_final: 0.6005 (tt0) REVERT: B 763 LYS cc_start: 0.6581 (mptt) cc_final: 0.6178 (mptt) REVERT: B 765 ASN cc_start: 0.4777 (OUTLIER) cc_final: 0.1524 (t0) REVERT: B 976 MET cc_start: 0.6356 (tmm) cc_final: 0.5759 (tmm) REVERT: F 51 TYR cc_start: 0.5675 (t80) cc_final: 0.4803 (t80) REVERT: F 75 MET cc_start: 0.6935 (ptm) cc_final: 0.6597 (ptt) outliers start: 55 outliers final: 38 residues processed: 247 average time/residue: 0.1096 time to fit residues: 41.0407 Evaluate side-chains 246 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 957 SER Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 552 TYR Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain F residue 67 PHE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 235 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 20 optimal weight: 0.0170 chunk 73 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN A 503 HIS ** F 34 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 = 0.4792 r_free = 0.4792 target = 0.250224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.216700 restraints weight = 17242.705| |-----------------------------------------------------------------------------| r_work (start): 0.4486 rms_B_bonded: 2.24 r_work: 0.4349 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14382 Z= 0.121 Angle : 0.529 7.592 19350 Z= 0.284 Chirality : 0.040 0.250 2052 Planarity : 0.003 0.052 2480 Dihedral : 4.264 27.217 1858 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.75 % Allowed : 22.96 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.20), residues: 1682 helix: 0.95 (0.17), residues: 963 sheet: -1.10 (0.47), residues: 100 loop : -1.49 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 870 TYR 0.047 0.002 TYR A 625 PHE 0.033 0.001 PHE A 387 TRP 0.009 0.001 TRP B 601 HIS 0.011 0.001 HIS B 852 Details of bonding type rmsd covalent geometry : bond 0.00275 (14382) covalent geometry : angle 0.52946 (19350) hydrogen bonds : bond 0.03385 ( 755) hydrogen bonds : angle 4.53574 ( 2172) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 219 time to evaluate : 0.523 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 306 ASP cc_start: 0.5262 (OUTLIER) cc_final: 0.4949 (t0) REVERT: A 364 LYS cc_start: 0.7651 (tttt) cc_final: 0.6710 (ttmt) REVERT: A 389 GLU cc_start: 0.6999 (pp20) cc_final: 0.6785 (pp20) REVERT: A 503 HIS cc_start: 0.7770 (OUTLIER) cc_final: 0.6563 (p-80) REVERT: A 569 MET cc_start: 0.6396 (OUTLIER) cc_final: 0.4316 (mtt) REVERT: A 616 MET cc_start: 0.8413 (mmm) cc_final: 0.8202 (mmm) REVERT: A 626 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: A 647 MET cc_start: 0.6937 (tpt) cc_final: 0.4974 (tpt) REVERT: A 687 TYR cc_start: 0.7050 (OUTLIER) cc_final: 0.5446 (t80) REVERT: A 722 PHE cc_start: 0.6634 (t80) cc_final: 0.6398 (t80) REVERT: A 807 LEU cc_start: 0.5636 (OUTLIER) cc_final: 0.5241 (tp) REVERT: A 950 ASP cc_start: 0.6957 (p0) cc_final: 0.6642 (p0) REVERT: A 1001 MET cc_start: 0.5834 (mmm) cc_final: 0.5577 (mmm) REVERT: B 331 LYS cc_start: 0.7482 (ptpt) cc_final: 0.7267 (pttp) REVERT: B 552 TYR cc_start: 0.6188 (OUTLIER) cc_final: 0.5153 (t80) REVERT: B 562 THR cc_start: 0.7726 (m) cc_final: 0.7446 (p) REVERT: B 624 GLU cc_start: 0.5835 (tp30) cc_final: 0.5602 (tp30) REVERT: B 711 GLN cc_start: 0.6268 (tm-30) cc_final: 0.5934 (tt0) REVERT: B 763 LYS cc_start: 0.6571 (mptt) cc_final: 0.6144 (mptt) REVERT: B 765 ASN cc_start: 0.4793 (OUTLIER) cc_final: 0.1580 (t0) REVERT: B 976 MET cc_start: 0.5983 (tmm) cc_final: 0.5539 (tmm) REVERT: B 986 GLU cc_start: 0.6850 (pp20) cc_final: 0.6619 (pp20) REVERT: F 75 MET cc_start: 0.6882 (ptm) cc_final: 0.6549 (ptt) REVERT: F 231 MET cc_start: 0.2436 (pmm) cc_final: 0.1784 (pmm) outliers start: 58 outliers final: 39 residues processed: 257 average time/residue: 0.1119 time to fit residues: 43.3426 Evaluate side-chains 251 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 204 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 957 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 552 TYR Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain F residue 67 PHE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 235 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 126 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 104 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 55 optimal weight: 0.0980 chunk 112 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 973 ASN B 852 HIS ** F 34 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 = 0.4760 r_free = 0.4760 target = 0.247227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.212105 restraints weight = 17377.427| |-----------------------------------------------------------------------------| r_work (start): 0.4476 rms_B_bonded: 2.28 r_work: 0.4339 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14382 Z= 0.123 Angle : 0.561 13.789 19350 Z= 0.293 Chirality : 0.040 0.280 2052 Planarity : 0.003 0.051 2480 Dihedral : 4.293 27.156 1858 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.75 % Allowed : 23.09 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.20), residues: 1682 helix: 0.97 (0.17), residues: 961 sheet: -1.34 (0.46), residues: 110 loop : -1.42 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 502 TYR 0.045 0.001 TYR A 625 PHE 0.028 0.001 PHE B 708 TRP 0.014 0.001 TRP B 601 HIS 0.010 0.001 HIS B 852 Details of bonding type rmsd covalent geometry : bond 0.00283 (14382) covalent geometry : angle 0.56060 (19350) hydrogen bonds : bond 0.03356 ( 755) hydrogen bonds : angle 4.52079 ( 2172) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 215 time to evaluate : 0.521 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 306 ASP cc_start: 0.5234 (OUTLIER) cc_final: 0.4936 (t0) REVERT: A 364 LYS cc_start: 0.7662 (tttt) cc_final: 0.6710 (ttmt) REVERT: A 389 GLU cc_start: 0.7047 (pp20) cc_final: 0.6788 (pp20) REVERT: A 569 MET cc_start: 0.6351 (OUTLIER) cc_final: 0.4395 (mtt) REVERT: A 616 MET cc_start: 0.8413 (mmm) cc_final: 0.8195 (mmm) REVERT: A 626 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7429 (mm-30) REVERT: A 647 MET cc_start: 0.6968 (tpt) cc_final: 0.5037 (tpt) REVERT: A 687 TYR cc_start: 0.7108 (OUTLIER) cc_final: 0.5471 (t80) REVERT: A 738 LYS cc_start: 0.7453 (mmmm) cc_final: 0.7237 (mmmt) REVERT: A 807 LEU cc_start: 0.5561 (OUTLIER) cc_final: 0.5175 (tp) REVERT: A 950 ASP cc_start: 0.6950 (p0) cc_final: 0.6622 (p0) REVERT: A 1001 MET cc_start: 0.5878 (mmm) cc_final: 0.5638 (mmm) REVERT: B 331 LYS cc_start: 0.7506 (ptpt) cc_final: 0.7265 (pttp) REVERT: B 384 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6850 (mm) REVERT: B 552 TYR cc_start: 0.6059 (OUTLIER) cc_final: 0.5046 (t80) REVERT: B 624 GLU cc_start: 0.5842 (tp30) cc_final: 0.5604 (tp30) REVERT: B 711 GLN cc_start: 0.6273 (tm-30) cc_final: 0.5916 (tt0) REVERT: B 763 LYS cc_start: 0.6579 (mptt) cc_final: 0.6109 (mptt) REVERT: B 765 ASN cc_start: 0.4812 (OUTLIER) cc_final: 0.1643 (t0) REVERT: B 976 MET cc_start: 0.6020 (tmm) cc_final: 0.5481 (tmm) REVERT: E 236 GLU cc_start: 0.4788 (OUTLIER) cc_final: 0.3631 (mp0) REVERT: F 75 MET cc_start: 0.6899 (ptm) cc_final: 0.6547 (ptt) REVERT: F 176 ARG cc_start: 0.4835 (tmm160) cc_final: 0.4312 (tmm160) REVERT: F 231 MET cc_start: 0.2433 (pmm) cc_final: 0.1808 (pmm) outliers start: 58 outliers final: 42 residues processed: 254 average time/residue: 0.1081 time to fit residues: 41.2581 Evaluate side-chains 254 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 203 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 367 CYS Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 957 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 552 TYR Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 31 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 67 PHE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 235 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 125 optimal weight: 9.9990 chunk 116 optimal weight: 0.0870 chunk 154 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 HIS A 503 HIS B 852 HIS B 979 HIS ** F 34 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 = 0.4787 r_free = 0.4787 target = 0.248393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.214895 restraints weight = 17093.902| |-----------------------------------------------------------------------------| r_work (start): 0.4476 rms_B_bonded: 2.19 r_work: 0.4342 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5933 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14382 Z= 0.132 Angle : 0.572 12.512 19350 Z= 0.304 Chirality : 0.041 0.355 2052 Planarity : 0.003 0.052 2480 Dihedral : 4.352 26.943 1858 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.88 % Allowed : 23.42 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.20), residues: 1682 helix: 0.88 (0.17), residues: 966 sheet: -1.30 (0.45), residues: 110 loop : -1.50 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 629 TYR 0.041 0.002 TYR A 625 PHE 0.034 0.002 PHE A 646 TRP 0.013 0.001 TRP B 601 HIS 0.011 0.001 HIS B 852 Details of bonding type rmsd covalent geometry : bond 0.00302 (14382) covalent geometry : angle 0.57164 (19350) hydrogen bonds : bond 0.03421 ( 755) hydrogen bonds : angle 4.52992 ( 2172) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 214 time to evaluate : 0.546 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 306 ASP cc_start: 0.5237 (OUTLIER) cc_final: 0.4934 (t0) REVERT: A 364 LYS cc_start: 0.7658 (tttt) cc_final: 0.6729 (ttmt) REVERT: A 389 GLU cc_start: 0.7167 (pp20) cc_final: 0.6911 (pp20) REVERT: A 569 MET cc_start: 0.6369 (OUTLIER) cc_final: 0.4530 (mtt) REVERT: A 616 MET cc_start: 0.8432 (mmm) cc_final: 0.8183 (mmm) REVERT: A 647 MET cc_start: 0.7097 (tpt) cc_final: 0.5437 (tpt) REVERT: A 687 TYR cc_start: 0.7051 (OUTLIER) cc_final: 0.5509 (t80) REVERT: A 738 LYS cc_start: 0.7449 (mmmm) cc_final: 0.7233 (mmmt) REVERT: A 950 ASP cc_start: 0.6913 (p0) cc_final: 0.6608 (p0) REVERT: A 1001 MET cc_start: 0.5801 (mmm) cc_final: 0.5585 (mmm) REVERT: B 552 TYR cc_start: 0.6102 (OUTLIER) cc_final: 0.5192 (t80) REVERT: B 624 GLU cc_start: 0.5832 (tp30) cc_final: 0.5564 (tp30) REVERT: B 711 GLN cc_start: 0.6338 (tm-30) cc_final: 0.5997 (tt0) REVERT: B 763 LYS cc_start: 0.6505 (mptt) cc_final: 0.6049 (mptt) REVERT: B 765 ASN cc_start: 0.4843 (OUTLIER) cc_final: 0.1846 (t0) REVERT: B 976 MET cc_start: 0.5948 (tmm) cc_final: 0.5254 (tmm) REVERT: F 75 MET cc_start: 0.6887 (ptm) cc_final: 0.6551 (ptt) REVERT: F 176 ARG cc_start: 0.4798 (tmm160) cc_final: 0.4350 (tmm160) REVERT: F 231 MET cc_start: 0.2509 (pmm) cc_final: 0.1814 (pmm) outliers start: 60 outliers final: 45 residues processed: 252 average time/residue: 0.0997 time to fit residues: 38.2470 Evaluate side-chains 260 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 210 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 957 SER Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 552 TYR Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain F residue 67 PHE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 235 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 30 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 137 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 852 HIS B 979 HIS ** F 34 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 = 0.4773 r_free = 0.4773 target = 0.248101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.213908 restraints weight = 17188.369| |-----------------------------------------------------------------------------| r_work (start): 0.4470 rms_B_bonded: 2.24 r_work: 0.4335 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14382 Z= 0.138 Angle : 0.582 12.485 19350 Z= 0.309 Chirality : 0.041 0.332 2052 Planarity : 0.004 0.052 2480 Dihedral : 4.378 27.030 1858 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.36 % Allowed : 24.32 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.20), residues: 1682 helix: 0.83 (0.17), residues: 958 sheet: -1.30 (0.44), residues: 110 loop : -1.54 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 480 TYR 0.051 0.002 TYR A 625 PHE 0.034 0.002 PHE A 646 TRP 0.011 0.001 TRP B 601 HIS 0.012 0.001 HIS B 852 Details of bonding type rmsd covalent geometry : bond 0.00317 (14382) covalent geometry : angle 0.58206 (19350) hydrogen bonds : bond 0.03451 ( 755) hydrogen bonds : angle 4.57620 ( 2172) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 216 time to evaluate : 0.332 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 306 ASP cc_start: 0.5232 (OUTLIER) cc_final: 0.4959 (t0) REVERT: A 364 LYS cc_start: 0.7666 (tttt) cc_final: 0.6741 (ttmt) REVERT: A 384 LEU cc_start: 0.7621 (tp) cc_final: 0.7292 (mm) REVERT: A 389 GLU cc_start: 0.7159 (pp20) cc_final: 0.6912 (pp20) REVERT: A 569 MET cc_start: 0.6389 (OUTLIER) cc_final: 0.4489 (mtt) REVERT: A 616 MET cc_start: 0.8404 (mmm) cc_final: 0.8145 (mmm) REVERT: A 647 MET cc_start: 0.7051 (tpt) cc_final: 0.5372 (tpt) REVERT: A 687 TYR cc_start: 0.7092 (OUTLIER) cc_final: 0.5458 (t80) REVERT: A 738 LYS cc_start: 0.7491 (mmmm) cc_final: 0.7275 (mmmt) REVERT: A 950 ASP cc_start: 0.6857 (p0) cc_final: 0.6574 (p0) REVERT: B 390 LYS cc_start: 0.6601 (ttpt) cc_final: 0.5889 (pttt) REVERT: B 420 VAL cc_start: 0.7362 (t) cc_final: 0.6924 (p) REVERT: B 585 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.7035 (tp) REVERT: B 624 GLU cc_start: 0.5714 (tp30) cc_final: 0.5486 (tp30) REVERT: B 711 GLN cc_start: 0.6357 (tm-30) cc_final: 0.5977 (tt0) REVERT: B 765 ASN cc_start: 0.4870 (OUTLIER) cc_final: 0.1916 (t0) REVERT: E 206 MET cc_start: 0.5650 (mtm) cc_final: 0.5352 (mtm) REVERT: F 75 MET cc_start: 0.6803 (ptm) cc_final: 0.6437 (ptt) REVERT: F 231 MET cc_start: 0.2504 (pmm) cc_final: 0.1962 (pmm) outliers start: 52 outliers final: 40 residues processed: 250 average time/residue: 0.0911 time to fit residues: 34.6956 Evaluate side-chains 249 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 204 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 957 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain F residue 67 PHE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 235 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 105 optimal weight: 0.6980 chunk 152 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 HIS A 895 ASN B 852 HIS B 979 HIS ** F 34 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 = 0.4769 r_free = 0.4769 target = 0.246540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.212804 restraints weight = 17096.553| |-----------------------------------------------------------------------------| r_work (start): 0.4464 rms_B_bonded: 2.17 r_work: 0.4330 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14382 Z= 0.144 Angle : 0.597 12.502 19350 Z= 0.317 Chirality : 0.042 0.349 2052 Planarity : 0.004 0.053 2480 Dihedral : 4.425 27.117 1858 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.49 % Allowed : 24.19 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.20), residues: 1682 helix: 0.74 (0.17), residues: 967 sheet: -1.28 (0.44), residues: 110 loop : -1.63 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 480 TYR 0.039 0.002 TYR A 625 PHE 0.034 0.002 PHE A 646 TRP 0.011 0.001 TRP B 601 HIS 0.012 0.001 HIS B 852 Details of bonding type rmsd covalent geometry : bond 0.00332 (14382) covalent geometry : angle 0.59740 (19350) hydrogen bonds : bond 0.03514 ( 755) hydrogen bonds : angle 4.60874 ( 2172) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 214 time to evaluate : 0.347 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 306 ASP cc_start: 0.5202 (OUTLIER) cc_final: 0.4934 (t0) REVERT: A 364 LYS cc_start: 0.7690 (tttt) cc_final: 0.6732 (ttmt) REVERT: A 384 LEU cc_start: 0.7621 (tp) cc_final: 0.7310 (mm) REVERT: A 569 MET cc_start: 0.6208 (OUTLIER) cc_final: 0.4291 (mtt) REVERT: A 616 MET cc_start: 0.8417 (mmm) cc_final: 0.8166 (mmm) REVERT: A 647 MET cc_start: 0.7177 (tpt) cc_final: 0.5465 (tpt) REVERT: A 687 TYR cc_start: 0.7119 (OUTLIER) cc_final: 0.5464 (t80) REVERT: A 738 LYS cc_start: 0.7521 (mmmm) cc_final: 0.7307 (mmmt) REVERT: A 950 ASP cc_start: 0.6818 (p0) cc_final: 0.6526 (p0) REVERT: B 390 LYS cc_start: 0.6630 (ttpt) cc_final: 0.5972 (pttt) REVERT: B 585 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6922 (tp) REVERT: B 624 GLU cc_start: 0.5787 (tp30) cc_final: 0.5555 (tp30) REVERT: B 693 GLU cc_start: 0.5476 (mp0) cc_final: 0.4774 (mm-30) REVERT: B 765 ASN cc_start: 0.5011 (OUTLIER) cc_final: 0.2158 (t0) REVERT: F 75 MET cc_start: 0.6763 (ptm) cc_final: 0.6401 (ptt) REVERT: F 176 ARG cc_start: 0.4586 (tmm160) cc_final: 0.4041 (tmm160) REVERT: F 231 MET cc_start: 0.2626 (pmm) cc_final: 0.2168 (pmm) outliers start: 54 outliers final: 42 residues processed: 246 average time/residue: 0.0923 time to fit residues: 33.9097 Evaluate side-chains 257 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 687 TYR Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 957 SER Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain F residue 67 PHE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 235 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 164 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 79 optimal weight: 6.9990 chunk 11 optimal weight: 0.0470 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 852 HIS B 979 HIS ** F 34 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 = 0.4788 r_free = 0.4788 target = 0.248811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.215498 restraints weight = 17128.586| |-----------------------------------------------------------------------------| r_work (start): 0.4491 rms_B_bonded: 2.18 r_work: 0.4360 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 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 0.039 14382 Z= 0.125 Angle : 0.591 11.855 19350 Z= 0.315 Chirality : 0.041 0.295 2052 Planarity : 0.003 0.053 2480 Dihedral : 4.366 27.175 1858 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.72 % Allowed : 24.77 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.20), residues: 1682 helix: 0.81 (0.17), residues: 965 sheet: -1.20 (0.44), residues: 110 loop : -1.59 (0.23), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 502 TYR 0.032 0.002 TYR A 552 PHE 0.034 0.001 PHE A 646 TRP 0.010 0.001 TRP B 601 HIS 0.013 0.001 HIS B 852 Details of bonding type rmsd covalent geometry : bond 0.00281 (14382) covalent geometry : angle 0.59133 (19350) hydrogen bonds : bond 0.03352 ( 755) hydrogen bonds : angle 4.54161 ( 2172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2773.79 seconds wall clock time: 48 minutes 41.01 seconds (2921.01 seconds total)