Starting phenix.real_space_refine on Sun Jan 19 15:40:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ztr_60470/01_2025/8ztr_60470.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ztr_60470/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ztr_60470/01_2025/8ztr_60470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ztr_60470/01_2025/8ztr_60470.map" model { file = "/net/cci-nas-00/data/ceres_data/8ztr_60470/01_2025/8ztr_60470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ztr_60470/01_2025/8ztr_60470.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 8.62, per 1000 atoms: 0.61 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: 3.28 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.53 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: 4.47 Time building geometry restraints manager: 3.84 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 32.580 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.650 ------------------------------------------------------------------------------- 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= 0.289 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.008 0.001 TRP B 958 HIS 0.004 0.001 HIS A 786 PHE 0.041 0.002 PHE F 32 TYR 0.038 0.002 TYR B1003 ARG 0.005 0.001 ARG A 447 *********************** 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 : 1.359 Fit side-chains revert: symmetry clash 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: 0.6357 (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: 0.5352 (mm-30) REVERT: F 219 LYS cc_start: 0.8026 (mtpp) cc_final: 0.7631 (mtpp) outliers start: 7 outliers final: 2 residues processed: 224 average time/residue: 0.2753 time to fit residues: 90.5226 Evaluate side-chains 189 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 187 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 231 MET 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 141 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 43 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 152 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4798 r_free = 0.4798 target = 0.250033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.216775 restraints weight = 17359.812| |-----------------------------------------------------------------------------| r_work (start): 0.4478 rms_B_bonded: 2.24 r_work: 0.4340 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14382 Z= 0.208 Angle : 0.587 11.503 19350 Z= 0.312 Chirality : 0.041 0.287 2052 Planarity : 0.004 0.076 2480 Dihedral : 4.650 33.251 1862 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.98 % Allowed : 20.38 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.20), residues: 1682 helix: 0.84 (0.17), residues: 963 sheet: -1.70 (0.46), residues: 102 loop : -1.56 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 958 HIS 0.007 0.001 HIS B 852 PHE 0.016 0.002 PHE A 708 TYR 0.016 0.002 TYR B 951 ARG 0.006 0.001 ARG A 870 *********************** 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 266 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 220 time to evaluate : 1.674 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: 0.5343 (OUTLIER) cc_final: 0.4984 (t0) REVERT: A 381 PHE cc_start: 0.8003 (t80) cc_final: 0.7716 (t80) REVERT: A 616 MET cc_start: 0.8404 (mmm) cc_final: 0.8119 (mmm) REVERT: A 626 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7654 (mm-30) REVERT: A 663 ASP cc_start: 0.5730 (m-30) cc_final: 0.5408 (m-30) REVERT: A 950 ASP cc_start: 0.7000 (p0) cc_final: 0.6677 (p0) REVERT: B 331 LYS cc_start: 0.7514 (ptpt) cc_final: 0.7254 (pttp) REVERT: B 406 SER cc_start: 0.6500 (t) cc_final: 0.6257 (m) REVERT: B 544 PHE cc_start: 0.6405 (t80) cc_final: 0.6108 (t80) REVERT: B 552 TYR cc_start: 0.6193 (OUTLIER) cc_final: 0.5439 (t80) REVERT: B 562 THR cc_start: 0.7725 (m) cc_final: 0.7507 (p) REVERT: B 578 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7460 (ttp) REVERT: B 857 LYS cc_start: 0.5293 (tttt) cc_final: 0.4451 (ttmt) REVERT: B 964 ASP cc_start: 0.5076 (m-30) cc_final: 0.4866 (t70) outliers start: 46 outliers final: 21 residues processed: 248 average time/residue: 0.2919 time to fit residues: 104.9932 Evaluate side-chains 219 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 1.558 ------------------------------------------------------------------------------- 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 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 235 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 95 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 0.1980 chunk 149 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 48 optimal weight: 0.0980 chunk 162 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 HIS A 503 HIS ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN B 698 GLN B 852 HIS B 961 ASN E 210 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.246337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.212582 restraints weight = 17350.624| |-----------------------------------------------------------------------------| r_work (start): 0.4448 rms_B_bonded: 2.22 r_work: 0.4312 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14382 Z= 0.218 Angle : 0.575 10.870 19350 Z= 0.307 Chirality : 0.041 0.248 2052 Planarity : 0.004 0.076 2480 Dihedral : 4.447 29.249 1858 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.69 % Allowed : 20.76 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1682 helix: 0.76 (0.16), residues: 966 sheet: -1.54 (0.46), residues: 102 loop : -1.59 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 958 HIS 0.007 0.001 HIS B 852 PHE 0.025 0.002 PHE A 387 TYR 0.021 0.002 TYR A 625 ARG 0.004 0.000 ARG A 480 *********************** 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 269 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 212 time to evaluate : 1.444 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: 0.5303 (OUTLIER) cc_final: 0.4931 (t0) REVERT: A 364 LYS cc_start: 0.7625 (tttt) cc_final: 0.6643 (ttmt) REVERT: A 381 PHE cc_start: 0.8001 (t80) cc_final: 0.7684 (t80) REVERT: A 503 HIS cc_start: 0.7523 (OUTLIER) cc_final: 0.6843 (p-80) REVERT: A 616 MET cc_start: 0.8413 (mmm) cc_final: 0.8171 (mmm) REVERT: A 626 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7458 (mm-30) REVERT: A 663 ASP cc_start: 0.5805 (m-30) cc_final: 0.5414 (m-30) REVERT: A 802 ARG cc_start: 0.6067 (ptt180) cc_final: 0.5104 (ptp90) REVERT: A 950 ASP cc_start: 0.7001 (p0) cc_final: 0.6641 (p0) REVERT: A 1001 MET cc_start: 0.5920 (mmm) cc_final: 0.5526 (mmm) REVERT: B 331 LYS cc_start: 0.7502 (ptpt) cc_final: 0.7281 (pttp) REVERT: B 406 SER cc_start: 0.6500 (t) cc_final: 0.6298 (m) REVERT: B 552 TYR cc_start: 0.6191 (OUTLIER) cc_final: 0.4878 (t80) REVERT: B 562 THR cc_start: 0.7808 (m) cc_final: 0.7468 (p) REVERT: B 765 ASN cc_start: 0.4753 (OUTLIER) cc_final: 0.1527 (t0) REVERT: B 964 ASP cc_start: 0.5177 (m-30) cc_final: 0.4952 (t70) REVERT: B 976 MET cc_start: 0.6243 (tmm) cc_final: 0.5887 (tmm) REVERT: E 206 MET cc_start: 0.5417 (mmm) cc_final: 0.4866 (mtp) REVERT: F 75 MET cc_start: 0.6902 (ptm) cc_final: 0.6558 (ptt) REVERT: F 176 ARG cc_start: 0.4941 (tmm160) cc_final: 0.4613 (ttp80) outliers start: 57 outliers final: 29 residues processed: 247 average time/residue: 0.2824 time to fit residues: 104.1823 Evaluate side-chains 226 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 1.642 ------------------------------------------------------------------------------- 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 807 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 346 VAL 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 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 825 LEU Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 891 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 E residue 228 THR 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 138 optimal weight: 0.4980 chunk 139 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 A 895 ASN B 483 GLN B 852 HIS ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.247316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.213527 restraints weight = 17099.133| |-----------------------------------------------------------------------------| r_work (start): 0.4458 rms_B_bonded: 2.20 r_work: 0.4326 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 moved from start: 0.2551 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= 0.186 Angle : 0.546 10.606 19350 Z= 0.292 Chirality : 0.040 0.218 2052 Planarity : 0.004 0.077 2480 Dihedral : 4.376 27.575 1858 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.88 % Allowed : 21.28 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.20), residues: 1682 helix: 0.83 (0.16), residues: 967 sheet: -1.49 (0.46), residues: 102 loop : -1.58 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 958 HIS 0.008 0.001 HIS B 852 PHE 0.027 0.001 PHE A 646 TYR 0.034 0.002 TYR A 625 ARG 0.003 0.000 ARG E 176 *********************** 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 268 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 208 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ASP cc_start: 0.5357 (OUTLIER) cc_final: 0.5021 (t0) REVERT: A 364 LYS cc_start: 0.7625 (tttt) cc_final: 0.6686 (ttmt) REVERT: A 503 HIS cc_start: 0.7604 (OUTLIER) cc_final: 0.6766 (p-80) REVERT: A 616 MET cc_start: 0.8433 (mmm) cc_final: 0.8183 (mmm) REVERT: A 626 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7683 (mm-30) REVERT: A 647 MET cc_start: 0.6928 (tpt) cc_final: 0.5258 (tpt) REVERT: A 687 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.5534 (t80) REVERT: A 950 ASP cc_start: 0.6940 (p0) cc_final: 0.6616 (p0) REVERT: A 1001 MET cc_start: 0.5961 (mmm) cc_final: 0.5620 (mmm) REVERT: B 331 LYS cc_start: 0.7508 (ptpt) cc_final: 0.7268 (pttp) REVERT: B 552 TYR cc_start: 0.6061 (OUTLIER) cc_final: 0.4857 (t80) REVERT: B 562 THR cc_start: 0.7725 (m) cc_final: 0.7412 (p) REVERT: B 624 GLU cc_start: 0.5884 (tp30) cc_final: 0.5602 (tp30) REVERT: B 763 LYS cc_start: 0.6665 (mptt) cc_final: 0.6318 (mptt) REVERT: B 765 ASN cc_start: 0.4723 (OUTLIER) cc_final: 0.1467 (t0) REVERT: B 964 ASP cc_start: 0.5133 (m-30) cc_final: 0.4911 (t0) REVERT: B 976 MET cc_start: 0.6297 (tmm) cc_final: 0.5952 (tmm) REVERT: F 75 MET cc_start: 0.6950 (ptm) cc_final: 0.6599 (ptt) outliers start: 60 outliers final: 37 residues processed: 251 average time/residue: 0.2793 time to fit residues: 104.6982 Evaluate side-chains 243 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 1.693 ------------------------------------------------------------------------------- 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 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 845 LEU Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain B residue 346 VAL 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 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 689 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 786 HIS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain E residue 29 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 82 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 138 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.247661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.213972 restraints weight = 17234.030| |-----------------------------------------------------------------------------| r_work (start): 0.4460 rms_B_bonded: 2.22 r_work: 0.4321 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5954 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14382 Z= 0.189 Angle : 0.548 10.342 19350 Z= 0.293 Chirality : 0.040 0.194 2052 Planarity : 0.003 0.075 2480 Dihedral : 4.376 27.249 1858 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.33 % Allowed : 21.80 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.20), residues: 1682 helix: 0.89 (0.17), residues: 960 sheet: -1.33 (0.47), residues: 102 loop : -1.50 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 958 HIS 0.010 0.001 HIS B 852 PHE 0.029 0.002 PHE A 387 TYR 0.041 0.001 TYR A 625 ARG 0.003 0.000 ARG E 176 *********************** 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 281 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 214 time to evaluate : 1.516 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: 0.5329 (OUTLIER) cc_final: 0.5006 (t0) REVERT: A 364 LYS cc_start: 0.7612 (tttt) cc_final: 0.6685 (ttmt) REVERT: A 381 PHE cc_start: 0.7801 (t80) cc_final: 0.7534 (t80) REVERT: A 503 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.6809 (p90) REVERT: A 616 MET cc_start: 0.8426 (mmm) cc_final: 0.8182 (mmm) REVERT: A 626 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7665 (mm-30) REVERT: A 647 MET cc_start: 0.7001 (tpt) cc_final: 0.5360 (tpt) REVERT: A 687 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.5390 (t80) REVERT: A 941 ASP cc_start: 0.5023 (m-30) cc_final: 0.4668 (m-30) REVERT: A 950 ASP cc_start: 0.6999 (p0) cc_final: 0.6649 (p0) REVERT: A 1001 MET cc_start: 0.5840 (mmm) cc_final: 0.5530 (mmm) REVERT: B 331 LYS cc_start: 0.7553 (ptpt) cc_final: 0.7320 (pttp) REVERT: B 396 MET cc_start: 0.6040 (mmm) cc_final: 0.5808 (tpp) REVERT: B 552 TYR cc_start: 0.6288 (OUTLIER) cc_final: 0.5173 (t80) REVERT: B 562 THR cc_start: 0.7761 (m) cc_final: 0.7435 (p) REVERT: B 624 GLU cc_start: 0.5869 (tp30) cc_final: 0.5628 (tp30) REVERT: B 711 GLN cc_start: 0.6504 (tm-30) cc_final: 0.6035 (tt0) REVERT: B 763 LYS cc_start: 0.6605 (mptt) cc_final: 0.6206 (mptt) REVERT: B 765 ASN cc_start: 0.4824 (OUTLIER) cc_final: 0.1590 (t0) REVERT: B 964 ASP cc_start: 0.5248 (m-30) cc_final: 0.4951 (t0) REVERT: B 976 MET cc_start: 0.6372 (tmm) cc_final: 0.5826 (tmm) REVERT: B 986 GLU cc_start: 0.7143 (pp20) cc_final: 0.6782 (pp20) REVERT: F 75 MET cc_start: 0.6942 (ptm) cc_final: 0.6619 (ptt) outliers start: 67 outliers final: 46 residues processed: 263 average time/residue: 0.2575 time to fit residues: 101.3499 Evaluate side-chains 257 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 1.455 ------------------------------------------------------------------------------- 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 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 845 LEU Chi-restraints excluded: chain A residue 853 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 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 786 HIS Chi-restraints excluded: chain B residue 825 LEU 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 B residue 950 ASP 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 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 22 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 53 optimal weight: 0.9980 chunk 52 optimal weight: 0.2980 chunk 12 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 152 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 HIS ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.247948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.214194 restraints weight = 17419.795| |-----------------------------------------------------------------------------| r_work (start): 0.4458 rms_B_bonded: 2.24 r_work: 0.4324 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14382 Z= 0.187 Angle : 0.555 12.129 19350 Z= 0.294 Chirality : 0.040 0.208 2052 Planarity : 0.004 0.074 2480 Dihedral : 4.387 26.959 1858 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.01 % Allowed : 22.57 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1682 helix: 0.88 (0.17), residues: 957 sheet: -1.27 (0.47), residues: 102 loop : -1.40 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 601 HIS 0.010 0.001 HIS B 852 PHE 0.040 0.002 PHE B 708 TYR 0.041 0.002 TYR A 625 ARG 0.002 0.000 ARG A 629 *********************** 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 281 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 219 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ASP cc_start: 0.5295 (OUTLIER) cc_final: 0.4994 (t0) REVERT: A 364 LYS cc_start: 0.7638 (tttt) cc_final: 0.6684 (ttmt) REVERT: A 381 PHE cc_start: 0.7807 (t80) cc_final: 0.7570 (t80) REVERT: A 616 MET cc_start: 0.8434 (mmm) cc_final: 0.8201 (mmm) REVERT: A 626 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7405 (mm-30) REVERT: A 647 MET cc_start: 0.7040 (tpt) cc_final: 0.5069 (tpt) REVERT: A 687 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.5480 (t80) REVERT: A 722 PHE cc_start: 0.6437 (t80) cc_final: 0.6228 (t80) REVERT: A 941 ASP cc_start: 0.5011 (m-30) cc_final: 0.4615 (m-30) REVERT: A 950 ASP cc_start: 0.6940 (p0) cc_final: 0.6619 (p0) REVERT: A 1001 MET cc_start: 0.5841 (mmm) cc_final: 0.5545 (mmm) REVERT: B 331 LYS cc_start: 0.7580 (ptpt) cc_final: 0.7366 (pttp) REVERT: B 552 TYR cc_start: 0.6174 (OUTLIER) cc_final: 0.5182 (t80) REVERT: B 562 THR cc_start: 0.7758 (m) cc_final: 0.7460 (p) REVERT: B 624 GLU cc_start: 0.5827 (tp30) cc_final: 0.5600 (tp30) REVERT: B 693 GLU cc_start: 0.5424 (mp0) cc_final: 0.5079 (mm-30) REVERT: B 711 GLN cc_start: 0.6351 (tm-30) cc_final: 0.5882 (tt0) REVERT: B 763 LYS cc_start: 0.6576 (mptt) cc_final: 0.6132 (mptt) REVERT: B 765 ASN cc_start: 0.4881 (OUTLIER) cc_final: 0.1656 (t0) REVERT: B 964 ASP cc_start: 0.5361 (m-30) cc_final: 0.5088 (t0) REVERT: B 976 MET cc_start: 0.6206 (tmm) cc_final: 0.5757 (tmm) REVERT: B 986 GLU cc_start: 0.7176 (pp20) cc_final: 0.6788 (pp20) REVERT: F 75 MET cc_start: 0.6899 (ptm) cc_final: 0.6576 (ptt) outliers start: 62 outliers final: 49 residues processed: 263 average time/residue: 0.2535 time to fit residues: 99.7650 Evaluate side-chains 256 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 202 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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 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 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 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 786 HIS Chi-restraints excluded: chain B residue 825 LEU 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 B residue 950 ASP 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 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 22 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 157 optimal weight: 0.0370 chunk 27 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 ASN B 852 HIS B 948 ASN 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 = 0.4775 r_free = 0.4775 target = 0.247086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.213703 restraints weight = 17256.694| |-----------------------------------------------------------------------------| r_work (start): 0.4475 rms_B_bonded: 2.18 r_work: 0.4341 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 moved from start: 0.3307 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= 0.188 Angle : 0.568 10.260 19350 Z= 0.300 Chirality : 0.040 0.206 2052 Planarity : 0.004 0.073 2480 Dihedral : 4.377 26.982 1858 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.20 % Allowed : 22.83 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.20), residues: 1682 helix: 0.92 (0.17), residues: 954 sheet: -1.16 (0.48), residues: 102 loop : -1.39 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 601 HIS 0.010 0.001 HIS B 852 PHE 0.036 0.002 PHE B 712 TYR 0.044 0.002 TYR A 625 ARG 0.005 0.000 ARG A 502 *********************** 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 280 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 215 time to evaluate : 1.575 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: 0.5347 (OUTLIER) cc_final: 0.5093 (t0) REVERT: A 364 LYS cc_start: 0.7680 (tttt) cc_final: 0.6788 (ttmt) REVERT: A 384 LEU cc_start: 0.7542 (tp) cc_final: 0.7243 (mm) REVERT: A 569 MET cc_start: 0.6445 (OUTLIER) cc_final: 0.5049 (mmt) REVERT: A 616 MET cc_start: 0.8393 (mmm) cc_final: 0.8114 (mmm) REVERT: A 647 MET cc_start: 0.7096 (tpt) cc_final: 0.5421 (tpt) REVERT: A 687 TYR cc_start: 0.7103 (OUTLIER) cc_final: 0.5535 (t80) REVERT: A 738 LYS cc_start: 0.7452 (mmmm) cc_final: 0.7235 (mmmt) REVERT: A 950 ASP cc_start: 0.6842 (p0) cc_final: 0.6568 (p0) REVERT: A 1001 MET cc_start: 0.5815 (mmm) cc_final: 0.5572 (mmm) REVERT: B 384 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6913 (mm) REVERT: B 531 MET cc_start: 0.5992 (mtp) cc_final: 0.5634 (mtp) REVERT: B 562 THR cc_start: 0.7805 (m) cc_final: 0.7491 (p) REVERT: B 624 GLU cc_start: 0.5798 (tp30) cc_final: 0.5585 (tp30) REVERT: B 711 GLN cc_start: 0.6530 (tm-30) cc_final: 0.6147 (tt0) REVERT: B 763 LYS cc_start: 0.6533 (mptt) cc_final: 0.6160 (mptt) REVERT: B 963 ASN cc_start: 0.5564 (m110) cc_final: 0.5276 (m-40) REVERT: B 976 MET cc_start: 0.5905 (tmm) cc_final: 0.5372 (tmm) REVERT: B 986 GLU cc_start: 0.7223 (pp20) cc_final: 0.6869 (pp20) REVERT: F 75 MET cc_start: 0.6854 (ptm) cc_final: 0.6517 (ptt) REVERT: F 176 ARG cc_start: 0.4830 (tmm160) cc_final: 0.4328 (tmm160) REVERT: F 231 MET cc_start: 0.2475 (pmm) cc_final: 0.1857 (pmm) outliers start: 65 outliers final: 52 residues processed: 255 average time/residue: 0.2728 time to fit residues: 103.4663 Evaluate side-chains 262 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 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 673 ILE 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 367 CYS 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 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 786 HIS Chi-restraints excluded: chain B residue 825 LEU 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 B residue 936 MET Chi-restraints excluded: chain B residue 948 ASN Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 31 SER 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 E residue 223 LEU Chi-restraints excluded: chain F residue 22 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 55 optimal weight: 7.9990 chunk 151 optimal weight: 0.4980 chunk 46 optimal weight: 0.2980 chunk 62 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 134 optimal weight: 0.0060 chunk 85 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 125 optimal weight: 20.0000 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 = 0.246829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.213688 restraints weight = 17151.756| |-----------------------------------------------------------------------------| r_work (start): 0.4464 rms_B_bonded: 2.17 r_work: 0.4333 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 moved from start: 0.3489 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= 0.193 Angle : 0.574 9.722 19350 Z= 0.305 Chirality : 0.041 0.368 2052 Planarity : 0.004 0.074 2480 Dihedral : 4.375 26.820 1858 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.27 % Allowed : 22.96 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1682 helix: 0.89 (0.17), residues: 953 sheet: -1.15 (0.48), residues: 102 loop : -1.38 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 601 HIS 0.011 0.001 HIS B 852 PHE 0.036 0.002 PHE A 646 TYR 0.036 0.002 TYR A 625 ARG 0.004 0.000 ARG A 613 *********************** 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 276 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 210 time to evaluate : 1.528 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: 0.5222 (OUTLIER) cc_final: 0.4944 (t0) REVERT: A 364 LYS cc_start: 0.7676 (tttt) cc_final: 0.6748 (ttmt) REVERT: A 384 LEU cc_start: 0.7549 (tp) cc_final: 0.7269 (mm) REVERT: A 569 MET cc_start: 0.6200 (OUTLIER) cc_final: 0.3998 (mpp) REVERT: A 616 MET cc_start: 0.8397 (mmm) cc_final: 0.8114 (mmm) REVERT: A 647 MET cc_start: 0.7167 (tpt) cc_final: 0.5487 (tpt) REVERT: A 687 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.5409 (t80) REVERT: A 722 PHE cc_start: 0.6425 (t80) cc_final: 0.6176 (t80) REVERT: A 738 LYS cc_start: 0.7492 (mmmm) cc_final: 0.7255 (mmmt) REVERT: A 950 ASP cc_start: 0.6938 (p0) cc_final: 0.6616 (p0) REVERT: A 1001 MET cc_start: 0.5881 (mmm) cc_final: 0.5617 (mmm) REVERT: B 396 MET cc_start: 0.5829 (mmm) cc_final: 0.5494 (tpp) REVERT: B 585 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6984 (tp) REVERT: B 624 GLU cc_start: 0.5879 (tp30) cc_final: 0.5664 (tp30) REVERT: B 711 GLN cc_start: 0.6332 (tm-30) cc_final: 0.5979 (tt0) REVERT: B 986 GLU cc_start: 0.7373 (pp20) cc_final: 0.6986 (pp20) REVERT: F 75 MET cc_start: 0.6943 (ptm) cc_final: 0.6613 (ptt) REVERT: F 176 ARG cc_start: 0.4829 (tmm160) cc_final: 0.4375 (tmm160) REVERT: F 231 MET cc_start: 0.2580 (pmm) cc_final: 0.1953 (pmm) outliers start: 66 outliers final: 53 residues processed: 254 average time/residue: 0.2564 time to fit residues: 97.4772 Evaluate side-chains 262 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 205 time to evaluate : 1.484 ------------------------------------------------------------------------------- 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 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 673 ILE 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 874 ILE 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 337 ASP Chi-restraints excluded: chain B residue 367 CYS 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 585 LEU 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 786 HIS Chi-restraints excluded: chain B residue 825 LEU 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 B residue 936 MET Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 31 SER 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 E residue 223 LEU Chi-restraints excluded: chain F residue 22 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 76 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.246431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.213252 restraints weight = 17125.440| |-----------------------------------------------------------------------------| r_work (start): 0.4471 rms_B_bonded: 2.16 r_work: 0.4336 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5975 moved from start: 0.3678 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= 0.197 Angle : 0.592 15.430 19350 Z= 0.311 Chirality : 0.042 0.330 2052 Planarity : 0.004 0.073 2480 Dihedral : 4.409 27.168 1858 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.27 % Allowed : 22.90 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.20), residues: 1682 helix: 0.86 (0.17), residues: 952 sheet: -1.19 (0.47), residues: 102 loop : -1.45 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 601 HIS 0.012 0.001 HIS B 852 PHE 0.035 0.002 PHE A 646 TYR 0.048 0.002 TYR A 625 ARG 0.005 0.000 ARG A 480 *********************** 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 277 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 211 time to evaluate : 1.566 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: 0.5150 (OUTLIER) cc_final: 0.4838 (t0) REVERT: A 364 LYS cc_start: 0.7669 (tttt) cc_final: 0.6718 (ttmt) REVERT: A 384 LEU cc_start: 0.7606 (tp) cc_final: 0.7309 (mm) REVERT: A 569 MET cc_start: 0.6260 (OUTLIER) cc_final: 0.3564 (mtt) REVERT: A 616 MET cc_start: 0.8374 (mmm) cc_final: 0.8137 (mmm) REVERT: A 647 MET cc_start: 0.7169 (tpt) cc_final: 0.5371 (tpt) REVERT: A 687 TYR cc_start: 0.7145 (OUTLIER) cc_final: 0.5594 (t80) REVERT: A 738 LYS cc_start: 0.7486 (mmmm) cc_final: 0.7264 (mmmt) REVERT: A 950 ASP cc_start: 0.6840 (p0) cc_final: 0.6557 (p0) REVERT: A 1001 MET cc_start: 0.5716 (mmm) cc_final: 0.5494 (mmm) REVERT: B 390 LYS cc_start: 0.6507 (ttpt) cc_final: 0.6033 (pttt) REVERT: B 420 VAL cc_start: 0.7425 (t) cc_final: 0.7178 (p) REVERT: B 624 GLU cc_start: 0.5798 (tp30) cc_final: 0.5413 (tp30) REVERT: B 986 GLU cc_start: 0.7312 (pp20) cc_final: 0.6968 (pp20) REVERT: E 75 MET cc_start: 0.3759 (ppp) cc_final: 0.3404 (ppp) REVERT: F 75 MET cc_start: 0.6746 (ptm) cc_final: 0.6413 (ptt) REVERT: F 231 MET cc_start: 0.2499 (pmm) cc_final: 0.1926 (pmm) outliers start: 66 outliers final: 52 residues processed: 253 average time/residue: 0.2758 time to fit residues: 102.9898 Evaluate side-chains 259 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 204 time to evaluate : 1.549 ------------------------------------------------------------------------------- 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 544 PHE Chi-restraints excluded: chain A residue 552 TYR 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 337 ASP Chi-restraints excluded: chain B residue 367 CYS 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 575 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 786 HIS Chi-restraints excluded: chain B residue 825 LEU 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 B residue 936 MET 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 E residue 223 LEU Chi-restraints excluded: chain F residue 22 VAL 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 208 LEU Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 136 optimal weight: 0.3980 chunk 120 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 HIS A 654 ASN A 895 ASN B 852 HIS B 979 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.249537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.216008 restraints weight = 17629.736| |-----------------------------------------------------------------------------| r_work (start): 0.4496 rms_B_bonded: 2.18 r_work: 0.4358 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.3877 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= 0.204 Angle : 0.602 14.286 19350 Z= 0.317 Chirality : 0.042 0.340 2052 Planarity : 0.004 0.074 2480 Dihedral : 4.409 26.899 1858 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.82 % Allowed : 23.54 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.20), residues: 1682 helix: 0.78 (0.16), residues: 961 sheet: -1.13 (0.47), residues: 108 loop : -1.46 (0.23), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 601 HIS 0.012 0.001 HIS B 852 PHE 0.034 0.002 PHE A 646 TYR 0.045 0.002 TYR A 625 ARG 0.005 0.000 ARG A 480 ********************** 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 271 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 212 time to evaluate : 1.561 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 364 LYS cc_start: 0.7598 (tttt) cc_final: 0.6640 (ttmt) REVERT: A 384 LEU cc_start: 0.7580 (tp) cc_final: 0.7316 (mm) REVERT: A 569 MET cc_start: 0.6220 (mpp) cc_final: 0.5205 (mpp) REVERT: A 616 MET cc_start: 0.8338 (mmm) cc_final: 0.8112 (mmm) REVERT: A 647 MET cc_start: 0.7132 (tpt) cc_final: 0.5286 (tpt) REVERT: A 687 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.5656 (t80) REVERT: A 950 ASP cc_start: 0.6777 (p0) cc_final: 0.6487 (p0) REVERT: A 1001 MET cc_start: 0.5730 (mmm) cc_final: 0.5508 (mmm) REVERT: B 390 LYS cc_start: 0.6679 (ttpt) cc_final: 0.6094 (pttt) REVERT: B 624 GLU cc_start: 0.5830 (tp30) cc_final: 0.5466 (tp30) REVERT: B 986 GLU cc_start: 0.7303 (pp20) cc_final: 0.6957 (pp20) REVERT: E 15 ARG cc_start: 0.6484 (ttt90) cc_final: 0.6217 (tmm-80) REVERT: F 75 MET cc_start: 0.6701 (ptm) cc_final: 0.6388 (ptt) REVERT: F 176 ARG cc_start: 0.4501 (tmm160) cc_final: 0.4043 (tmm160) outliers start: 59 outliers final: 50 residues processed: 250 average time/residue: 0.2806 time to fit residues: 103.9030 Evaluate side-chains 256 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 205 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 585 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 930 MET 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 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 575 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 786 HIS Chi-restraints excluded: chain B residue 825 LEU 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 B residue 936 MET 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 E residue 223 LEU Chi-restraints excluded: chain F residue 22 VAL 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 208 LEU Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 85 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 20 optimal weight: 0.0870 chunk 43 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 HIS F 34 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.251018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.217719 restraints weight = 17728.024| |-----------------------------------------------------------------------------| r_work (start): 0.4500 rms_B_bonded: 2.20 r_work: 0.4366 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 moved from start: 0.3988 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= 0.188 Angle : 0.600 14.097 19350 Z= 0.314 Chirality : 0.041 0.305 2052 Planarity : 0.004 0.073 2480 Dihedral : 4.418 27.124 1858 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.43 % Allowed : 24.19 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.20), residues: 1682 helix: 0.83 (0.17), residues: 957 sheet: -1.15 (0.46), residues: 102 loop : -1.50 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 958 HIS 0.012 0.001 HIS B 852 PHE 0.034 0.001 PHE A 646 TYR 0.049 0.002 TYR A 611 ARG 0.005 0.000 ARG A 502 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6270.03 seconds wall clock time: 114 minutes 0.06 seconds (6840.06 seconds total)