Starting phenix.real_space_refine on Thu Jun 12 12:56:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ztr_60470/06_2025/8ztr_60470.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ztr_60470/06_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_60470/06_2025/8ztr_60470.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ztr_60470/06_2025/8ztr_60470.map" model { file = "/net/cci-nas-00/data/ceres_data/8ztr_60470/06_2025/8ztr_60470.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ztr_60470/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.05, per 1000 atoms: 0.64 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: 3.53 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: 1.50 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: 4.56 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2391 1.31 - 1.44: 3992 1.44 - 1.56: 7907 1.56 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 14382 Sorted by residual: bond pdb=" C ASN A 598 " pdb=" O ASN A 598 " ideal model delta sigma weight residual 1.236 1.184 0.052 1.32e-02 5.74e+03 1.53e+01 bond pdb=" C ASN A 910 " pdb=" O ASN A 910 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.26e-02 6.30e+03 1.41e+01 bond pdb=" C ASP A 911 " pdb=" O ASP A 911 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.15e-02 7.56e+03 1.11e+01 bond pdb=" C ARG A 447 " pdb=" O ARG A 447 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.26e-02 6.30e+03 9.69e+00 bond pdb=" CA ASP A 788 " pdb=" C ASP A 788 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.32e-02 5.74e+03 8.07e+00 ... (remaining 14377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 18994 2.51 - 5.02: 313 5.02 - 7.53: 32 7.53 - 10.04: 8 10.04 - 12.55: 3 Bond angle restraints: 19350 Sorted by residual: angle pdb=" N LYS B 660 " pdb=" CA LYS B 660 " pdb=" C LYS B 660 " ideal model delta sigma weight residual 110.46 97.91 12.55 1.48e+00 4.57e-01 7.19e+01 angle pdb=" N PHE B 744 " pdb=" CA PHE B 744 " pdb=" C PHE B 744 " ideal model delta sigma weight residual 109.83 100.76 9.07 1.27e+00 6.20e-01 5.10e+01 angle pdb=" N ARG A 447 " pdb=" CA ARG A 447 " pdb=" C ARG A 447 " ideal model delta sigma weight residual 110.80 99.05 11.75 2.13e+00 2.20e-01 3.04e+01 angle pdb=" C ASN F 210 " pdb=" CA ASN F 210 " pdb=" CB ASN F 210 " ideal model delta sigma weight residual 110.08 101.63 8.45 1.57e+00 4.06e-01 2.90e+01 angle pdb=" N ASN A 702 " pdb=" CA ASN A 702 " pdb=" C ASN A 702 " ideal model delta sigma weight residual 111.28 105.89 5.39 1.09e+00 8.42e-01 2.45e+01 ... (remaining 19345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7329 17.98 - 35.96: 947 35.96 - 53.95: 253 53.95 - 71.93: 46 71.93 - 89.91: 21 Dihedral angle restraints: 8596 sinusoidal: 3574 harmonic: 5022 Sorted by residual: dihedral pdb=" C ASN F 210 " pdb=" N ASN F 210 " pdb=" CA ASN F 210 " pdb=" CB ASN F 210 " ideal model delta harmonic sigma weight residual -122.60 -112.10 -10.50 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" CA GLU F 230 " pdb=" C GLU F 230 " pdb=" N MET F 231 " pdb=" CA MET F 231 " ideal model delta harmonic sigma weight residual -180.00 -161.79 -18.21 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA THR E 8 " pdb=" C THR E 8 " pdb=" N ALA E 9 " pdb=" CA ALA E 9 " ideal model delta harmonic sigma weight residual 180.00 -162.09 -17.91 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 8593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1618 0.046 - 0.093: 333 0.093 - 0.139: 84 0.139 - 0.186: 13 0.186 - 0.232: 4 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CA TYR B1003 " pdb=" N TYR B1003 " pdb=" C TYR B1003 " pdb=" CB TYR B1003 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PHE A 907 " pdb=" N PHE A 907 " pdb=" C PHE A 907 " pdb=" CB PHE A 907 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ASN A 963 " pdb=" N ASN A 963 " pdb=" C ASN A 963 " pdb=" CB ASN A 963 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.62e-01 ... (remaining 2049 not shown) Planarity restraints: 2480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B1003 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C TYR B1003 " 0.062 2.00e-02 2.50e+03 pdb=" O TYR B1003 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE B1004 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 195 " -0.056 5.00e-02 4.00e+02 8.50e-02 1.16e+01 pdb=" N PRO E 196 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO E 196 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO E 196 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 409 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C ILE B 409 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE B 409 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN B 410 " -0.015 2.00e-02 2.50e+03 ... (remaining 2477 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1099 2.74 - 3.28: 15609 3.28 - 3.82: 24104 3.82 - 4.36: 28760 4.36 - 4.90: 48426 Nonbonded interactions: 117998 Sorted by model distance: nonbonded pdb=" O LEU A 551 " pdb=" OG1 THR A 555 " model vdw 2.195 3.040 nonbonded pdb=" O LYS B 785 " pdb=" NZ LYS B 785 " model vdw 2.207 3.120 nonbonded pdb=" OE2 GLU E 174 " pdb=" NH2 ARG E 176 " model vdw 2.230 3.120 nonbonded pdb=" O PHE A 559 " pdb=" OG1 THR A 562 " model vdw 2.236 3.040 nonbonded pdb=" O SER A 573 " pdb=" NH2 ARG A 629 " model vdw 2.237 3.120 ... (remaining 117993 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.770 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5810 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14382 Z= 0.260 Angle : 0.806 12.553 19350 Z= 0.476 Chirality : 0.043 0.232 2052 Planarity : 0.005 0.085 2480 Dihedral : 17.600 89.912 5364 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.76 % Favored : 95.18 % Rotamer: Outliers : 0.45 % Allowed : 19.66 % Favored : 79.88 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.15205 ( 755) hydrogen bonds : angle 6.16594 ( 2172) covalent geometry : bond 0.00452 (14382) covalent geometry : angle 0.80613 (19350) *********************** 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 : 1.515 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: 0.2604 time to fit residues: 85.5548 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 : 1.508 ------------------------------------------------------------------------------- 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 = 62)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.216760 restraints weight = 17359.764| |-----------------------------------------------------------------------------| r_work (start): 0.4479 rms_B_bonded: 2.24 r_work: 0.4340 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 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= 0.146 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 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 755) hydrogen bonds : angle 4.86067 ( 2172) covalent geometry : bond 0.00332 (14382) covalent geometry : angle 0.58698 (19350) *********************** 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 : 1.564 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: 0.5335 (OUTLIER) cc_final: 0.4978 (t0) REVERT: A 381 PHE cc_start: 0.8000 (t80) cc_final: 0.7714 (t80) REVERT: A 616 MET cc_start: 0.8401 (mmm) cc_final: 0.8116 (mmm) REVERT: A 626 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7659 (mm-30) REVERT: A 663 ASP cc_start: 0.5740 (m-30) cc_final: 0.5420 (m-30) REVERT: A 950 ASP cc_start: 0.7002 (p0) cc_final: 0.6678 (p0) REVERT: B 331 LYS cc_start: 0.7515 (ptpt) cc_final: 0.7250 (pttp) REVERT: B 406 SER cc_start: 0.6499 (t) cc_final: 0.6255 (m) REVERT: B 544 PHE cc_start: 0.6404 (t80) cc_final: 0.6106 (t80) REVERT: B 552 TYR cc_start: 0.6197 (OUTLIER) cc_final: 0.5441 (t80) REVERT: B 562 THR cc_start: 0.7726 (m) cc_final: 0.7506 (p) REVERT: B 578 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7459 (ttp) REVERT: B 857 LYS cc_start: 0.5295 (tttt) cc_final: 0.4454 (ttmt) REVERT: B 964 ASP cc_start: 0.5075 (m-30) cc_final: 0.4861 (t70) outliers start: 46 outliers final: 21 residues processed: 248 average time/residue: 0.2692 time to fit residues: 96.9205 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 : 1.485 ------------------------------------------------------------------------------- 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: 0.9990 chunk 124 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 0.0770 chunk 149 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- 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 = 0.4790 r_free = 0.4790 target = 0.247982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.215083 restraints weight = 17204.754| |-----------------------------------------------------------------------------| r_work (start): 0.4477 rms_B_bonded: 2.18 r_work: 0.4346 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5893 moved from start: 0.2117 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= 0.131 Angle : 0.552 10.842 19350 Z= 0.294 Chirality : 0.040 0.231 2052 Planarity : 0.003 0.074 2480 Dihedral : 4.363 29.769 1858 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.17 % Allowed : 20.76 % Favored : 76.07 % 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 (0.16), residues: 972 sheet: -1.49 (0.47), residues: 102 loop : -1.65 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 958 HIS 0.007 0.001 HIS B 852 PHE 0.023 0.001 PHE A 387 TYR 0.022 0.001 TYR A 625 ARG 0.003 0.000 ARG A 566 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 755) hydrogen bonds : angle 4.68245 ( 2172) covalent geometry : bond 0.00297 (14382) covalent geometry : angle 0.55221 (19350) *********************** 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 262 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 213 time to evaluate : 1.567 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: 0.5422 (OUTLIER) cc_final: 0.5038 (t0) REVERT: A 364 LYS cc_start: 0.7625 (tttt) cc_final: 0.6641 (ttmt) REVERT: A 503 HIS cc_start: 0.7314 (OUTLIER) cc_final: 0.7072 (p-80) REVERT: A 616 MET cc_start: 0.8361 (mmm) cc_final: 0.8114 (mmm) REVERT: A 626 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7551 (mm-30) REVERT: A 802 ARG cc_start: 0.6060 (ptt180) cc_final: 0.5015 (ptp90) REVERT: A 950 ASP cc_start: 0.6964 (p0) cc_final: 0.6622 (p0) REVERT: A 1001 MET cc_start: 0.5909 (mmm) cc_final: 0.5512 (mmm) REVERT: B 331 LYS cc_start: 0.7506 (ptpt) cc_final: 0.7277 (pttp) REVERT: B 544 PHE cc_start: 0.5741 (t80) cc_final: 0.5282 (t80) REVERT: B 552 TYR cc_start: 0.5976 (OUTLIER) cc_final: 0.4759 (t80) REVERT: B 562 THR cc_start: 0.7738 (m) cc_final: 0.7453 (p) REVERT: B 763 LYS cc_start: 0.6439 (mptt) cc_final: 0.6143 (mptt) REVERT: B 765 ASN cc_start: 0.4642 (OUTLIER) cc_final: 0.1406 (t0) REVERT: B 976 MET cc_start: 0.6146 (tmm) cc_final: 0.5827 (tmm) REVERT: E 206 MET cc_start: 0.5329 (mmm) cc_final: 0.4725 (mtp) REVERT: F 75 MET cc_start: 0.6988 (ptm) cc_final: 0.6640 (ptt) REVERT: F 176 ARG cc_start: 0.4995 (tmm160) cc_final: 0.4672 (ttp80) outliers start: 49 outliers final: 27 residues processed: 242 average time/residue: 0.2633 time to fit residues: 94.1740 Evaluate side-chains 230 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain B residue 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 531 MET Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 552 TYR Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 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: 0.7980 chunk 139 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 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: 0.5980 chunk 90 optimal weight: 0.7980 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 B 483 GLN B 852 HIS ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.249100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.215849 restraints weight = 17310.778| |-----------------------------------------------------------------------------| r_work (start): 0.4474 rms_B_bonded: 2.22 r_work: 0.4340 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 0.2451 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= 0.130 Angle : 0.550 12.506 19350 Z= 0.292 Chirality : 0.040 0.217 2052 Planarity : 0.003 0.074 2480 Dihedral : 4.348 27.777 1858 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.62 % Allowed : 21.09 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.16), residues: 966 sheet: -1.46 (0.46), residues: 102 loop : -1.63 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 958 HIS 0.008 0.001 HIS B 852 PHE 0.025 0.001 PHE A 387 TYR 0.035 0.002 TYR A 625 ARG 0.003 0.000 ARG A 480 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 755) hydrogen bonds : angle 4.62847 ( 2172) covalent geometry : bond 0.00299 (14382) covalent geometry : angle 0.54970 (19350) *********************** 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 265 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 209 time to evaluate : 1.645 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: 0.5383 (OUTLIER) cc_final: 0.5048 (t0) REVERT: A 364 LYS cc_start: 0.7644 (tttt) cc_final: 0.6703 (ttmt) REVERT: A 368 ASP cc_start: 0.8051 (p0) cc_final: 0.7835 (p0) REVERT: A 503 HIS cc_start: 0.7596 (OUTLIER) cc_final: 0.6827 (p-80) REVERT: A 616 MET cc_start: 0.8372 (mmm) cc_final: 0.8113 (mmm) REVERT: A 626 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7673 (mm-30) REVERT: A 647 MET cc_start: 0.6783 (tpt) cc_final: 0.5007 (tpt) REVERT: A 950 ASP cc_start: 0.6963 (p0) cc_final: 0.6638 (p0) REVERT: A 1001 MET cc_start: 0.5922 (mmm) cc_final: 0.5578 (mmm) REVERT: B 331 LYS cc_start: 0.7524 (ptpt) cc_final: 0.7296 (pttp) REVERT: B 552 TYR cc_start: 0.6061 (OUTLIER) cc_final: 0.4816 (t80) REVERT: B 562 THR cc_start: 0.7725 (m) cc_final: 0.7410 (p) REVERT: B 711 GLN cc_start: 0.6669 (tm-30) cc_final: 0.6209 (tt0) REVERT: B 765 ASN cc_start: 0.4699 (OUTLIER) cc_final: 0.1382 (t0) REVERT: B 976 MET cc_start: 0.6249 (tmm) cc_final: 0.5868 (tmm) REVERT: F 75 MET cc_start: 0.6986 (ptm) cc_final: 0.6615 (ptt) outliers start: 56 outliers final: 35 residues processed: 249 average time/residue: 0.2502 time to fit residues: 93.6212 Evaluate side-chains 233 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 193 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 845 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 531 MET Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 552 TYR Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 704 MET 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 866 MET Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain F residue 67 PHE Chi-restraints excluded: chain F residue 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: 3.9990 chunk 122 optimal weight: 10.0000 chunk 138 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 46 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 386 ASN A 491 GLN A 895 ASN B 852 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.248450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.214978 restraints weight = 17181.912| |-----------------------------------------------------------------------------| r_work (start): 0.4471 rms_B_bonded: 2.21 r_work: 0.4339 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14382 Z= 0.129 Angle : 0.548 10.442 19350 Z= 0.291 Chirality : 0.040 0.207 2052 Planarity : 0.003 0.072 2480 Dihedral : 4.333 27.410 1858 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.01 % Allowed : 21.93 % Favored : 74.06 % 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: 0.94 (0.17), residues: 955 sheet: -1.26 (0.47), residues: 102 loop : -1.49 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 601 HIS 0.009 0.001 HIS B 852 PHE 0.029 0.001 PHE A 646 TYR 0.044 0.001 TYR A 625 ARG 0.002 0.000 ARG A 480 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 755) hydrogen bonds : angle 4.59680 ( 2172) covalent geometry : bond 0.00298 (14382) covalent geometry : angle 0.54781 (19350) *********************** 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 271 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 209 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ASP cc_start: 0.5302 (OUTLIER) cc_final: 0.4986 (t0) REVERT: A 364 LYS cc_start: 0.7634 (tttt) cc_final: 0.6674 (ttmt) REVERT: A 503 HIS cc_start: 0.7403 (OUTLIER) cc_final: 0.6890 (p90) REVERT: A 616 MET cc_start: 0.8409 (mmm) cc_final: 0.8167 (mmm) REVERT: A 626 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7646 (mm-30) REVERT: A 647 MET cc_start: 0.6913 (tpt) cc_final: 0.5263 (tpt) REVERT: A 687 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.5644 (t80) REVERT: A 929 LYS cc_start: 0.6564 (tttm) cc_final: 0.6214 (tttm) REVERT: A 950 ASP cc_start: 0.6951 (p0) cc_final: 0.6624 (p0) REVERT: A 1001 MET cc_start: 0.5848 (mmm) cc_final: 0.5557 (mmm) REVERT: B 331 LYS cc_start: 0.7504 (ptpt) cc_final: 0.7278 (pttp) REVERT: B 552 TYR cc_start: 0.6059 (OUTLIER) cc_final: 0.4956 (t80) REVERT: B 562 THR cc_start: 0.7725 (m) cc_final: 0.7414 (p) REVERT: B 624 GLU cc_start: 0.5904 (tp30) cc_final: 0.5631 (tp30) REVERT: B 711 GLN cc_start: 0.6508 (tm-30) cc_final: 0.6029 (tt0) REVERT: B 763 LYS cc_start: 0.6642 (mptt) cc_final: 0.6331 (mptt) REVERT: B 765 ASN cc_start: 0.4790 (OUTLIER) cc_final: 0.1497 (t0) REVERT: B 976 MET cc_start: 0.6349 (tmm) cc_final: 0.5866 (tmm) REVERT: B 986 GLU cc_start: 0.6871 (pp20) cc_final: 0.6647 (pp20) REVERT: F 51 TYR cc_start: 0.5701 (t80) cc_final: 0.4807 (t80) REVERT: F 75 MET cc_start: 0.6944 (ptm) cc_final: 0.6592 (ptt) REVERT: F 219 LYS cc_start: 0.7749 (mtpp) cc_final: 0.7292 (mtpp) outliers start: 62 outliers final: 39 residues processed: 253 average time/residue: 0.2737 time to fit residues: 104.7996 Evaluate side-chains 244 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 1.980 ------------------------------------------------------------------------------- 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 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 B residue 451 SER Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 552 TYR Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 841 LEU 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 173 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain F residue 67 PHE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 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: 0.7980 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.4754 r_free = 0.4754 target = 0.245519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.211055 restraints weight = 17488.860| |-----------------------------------------------------------------------------| r_work (start): 0.4429 rms_B_bonded: 2.26 r_work: 0.4296 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 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 : 0.004 0.057 14382 Z= 0.155 Angle : 0.582 10.730 19350 Z= 0.308 Chirality : 0.041 0.193 2052 Planarity : 0.004 0.073 2480 Dihedral : 4.472 26.780 1858 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.27 % Allowed : 21.93 % Favored : 73.80 % 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: 0.77 (0.16), residues: 963 sheet: -1.27 (0.47), residues: 102 loop : -1.49 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 72 HIS 0.011 0.001 HIS B 852 PHE 0.044 0.002 PHE B 712 TYR 0.047 0.002 TYR A 625 ARG 0.005 0.000 ARG A 629 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 755) hydrogen bonds : angle 4.65510 ( 2172) covalent geometry : bond 0.00366 (14382) covalent geometry : angle 0.58150 (19350) *********************** 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 286 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 220 time to evaluate : 1.277 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: 0.5322 (OUTLIER) cc_final: 0.5035 (t0) REVERT: A 364 LYS cc_start: 0.7688 (tttt) cc_final: 0.6739 (ttmt) REVERT: A 384 LEU cc_start: 0.7595 (tp) cc_final: 0.7276 (mm) REVERT: A 442 LEU cc_start: 0.7000 (mt) cc_final: 0.6792 (mt) REVERT: A 616 MET cc_start: 0.8395 (mmm) cc_final: 0.8148 (mmm) REVERT: A 626 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7688 (mm-30) REVERT: A 647 MET cc_start: 0.7045 (tpt) cc_final: 0.5417 (tpt) REVERT: A 687 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.5618 (t80) REVERT: A 929 LYS cc_start: 0.6733 (tttm) cc_final: 0.6417 (tttm) REVERT: A 950 ASP cc_start: 0.6926 (p0) cc_final: 0.6601 (p0) REVERT: A 958 TRP cc_start: 0.6820 (OUTLIER) cc_final: 0.5995 (m-10) REVERT: A 1001 MET cc_start: 0.5860 (mmm) cc_final: 0.5578 (mmm) REVERT: B 552 TYR cc_start: 0.6302 (OUTLIER) cc_final: 0.5274 (t80) REVERT: B 562 THR cc_start: 0.7799 (m) cc_final: 0.7447 (p) REVERT: B 624 GLU cc_start: 0.5944 (tp30) cc_final: 0.5658 (tp30) REVERT: B 711 GLN cc_start: 0.6450 (tm-30) cc_final: 0.5979 (tt0) REVERT: B 763 LYS cc_start: 0.6641 (mptt) cc_final: 0.6222 (mptt) REVERT: B 765 ASN cc_start: 0.4859 (OUTLIER) cc_final: 0.1591 (t0) REVERT: B 976 MET cc_start: 0.6339 (tmm) cc_final: 0.5794 (tmm) REVERT: B 986 GLU cc_start: 0.7199 (pp20) cc_final: 0.6907 (pp20) REVERT: F 75 MET cc_start: 0.6951 (ptm) cc_final: 0.6607 (ptt) REVERT: F 231 MET cc_start: 0.2443 (pmm) cc_final: 0.1853 (pmm) outliers start: 66 outliers final: 45 residues processed: 264 average time/residue: 0.3874 time to fit residues: 158.0113 Evaluate side-chains 253 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 202 time to evaluate : 1.684 ------------------------------------------------------------------------------- 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 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 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 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 656 SER Chi-restraints excluded: chain B residue 660 LYS Chi-restraints excluded: chain B residue 676 ILE 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 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 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: 0.0870 chunk 27 optimal weight: 1.9990 chunk 146 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 127 optimal weight: 0.0050 chunk 40 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 overall best weight: 1.1376 ------------------------------------------------------------------------------- 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 ** 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 = 0.4750 r_free = 0.4750 target = 0.245327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.210745 restraints weight = 17411.833| |-----------------------------------------------------------------------------| r_work (start): 0.4435 rms_B_bonded: 2.23 r_work: 0.4300 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14382 Z= 0.158 Angle : 0.596 9.936 19350 Z= 0.316 Chirality : 0.041 0.202 2052 Planarity : 0.004 0.074 2480 Dihedral : 4.495 26.755 1858 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.53 % Allowed : 22.57 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.20), residues: 1682 helix: 0.70 (0.16), residues: 964 sheet: -1.74 (0.46), residues: 108 loop : -1.42 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 601 HIS 0.011 0.001 HIS B 852 PHE 0.047 0.002 PHE B 712 TYR 0.051 0.002 TYR A 625 ARG 0.004 0.000 ARG A 480 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 755) hydrogen bonds : angle 4.70166 ( 2172) covalent geometry : bond 0.00370 (14382) covalent geometry : angle 0.59613 (19350) *********************** 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 284 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 214 time to evaluate : 1.660 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: 0.5297 (OUTLIER) cc_final: 0.5015 (t0) REVERT: A 364 LYS cc_start: 0.7678 (tttt) cc_final: 0.6774 (ttmt) REVERT: A 384 LEU cc_start: 0.7627 (tp) cc_final: 0.7338 (mm) REVERT: A 569 MET cc_start: 0.6682 (OUTLIER) cc_final: 0.5316 (mmm) REVERT: A 616 MET cc_start: 0.8396 (mmm) cc_final: 0.8168 (mmm) REVERT: A 626 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7663 (mm-30) REVERT: A 647 MET cc_start: 0.7210 (tpt) cc_final: 0.5269 (tpt) REVERT: A 687 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.5624 (t80) REVERT: A 738 LYS cc_start: 0.7521 (mmmm) cc_final: 0.7297 (mmmt) REVERT: A 929 LYS cc_start: 0.6601 (tttm) cc_final: 0.6303 (tttm) REVERT: A 950 ASP cc_start: 0.6876 (p0) cc_final: 0.6561 (p0) REVERT: A 958 TRP cc_start: 0.6787 (OUTLIER) cc_final: 0.5943 (m-10) REVERT: B 384 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6836 (mm) REVERT: B 562 THR cc_start: 0.7817 (m) cc_final: 0.7461 (p) REVERT: B 624 GLU cc_start: 0.5901 (tp30) cc_final: 0.5671 (tp30) REVERT: B 711 GLN cc_start: 0.6560 (tm-30) cc_final: 0.6131 (tt0) REVERT: B 713 ILE cc_start: 0.6989 (tp) cc_final: 0.6604 (tp) REVERT: B 765 ASN cc_start: 0.4943 (OUTLIER) cc_final: 0.4067 (p0) REVERT: B 976 MET cc_start: 0.6112 (tmm) cc_final: 0.5669 (tmm) REVERT: B 986 GLU cc_start: 0.7168 (pp20) cc_final: 0.6895 (pp20) REVERT: F 75 MET cc_start: 0.6817 (ptm) cc_final: 0.6458 (ptt) REVERT: F 231 MET cc_start: 0.2421 (pmm) cc_final: 0.1845 (pmm) outliers start: 70 outliers final: 50 residues processed: 259 average time/residue: 0.3359 time to fit residues: 130.1240 Evaluate side-chains 263 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 206 time to evaluate : 1.588 ------------------------------------------------------------------------------- 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 328 ILE 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 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 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 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 740 LEU 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 866 MET Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 936 MET 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 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: 0.0070 chunk 151 optimal weight: 3.9990 chunk 46 optimal weight: 0.0980 chunk 62 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 HIS A 895 ASN B 852 HIS B 963 ASN B 979 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 = 0.4753 r_free = 0.4753 target = 0.244384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.210385 restraints weight = 17197.880| |-----------------------------------------------------------------------------| r_work (start): 0.4443 rms_B_bonded: 2.18 r_work: 0.4311 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.3578 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= 0.149 Angle : 0.599 9.401 19350 Z= 0.317 Chirality : 0.042 0.423 2052 Planarity : 0.004 0.074 2480 Dihedral : 4.515 26.677 1858 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.66 % Allowed : 22.57 % 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: -0.36 (0.20), residues: 1682 helix: 0.73 (0.17), residues: 956 sheet: -1.57 (0.45), residues: 112 loop : -1.48 (0.24), residues: 614 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 0.040 0.002 PHE B 708 TYR 0.051 0.002 TYR A 625 ARG 0.005 0.000 ARG A 480 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 755) hydrogen bonds : angle 4.66875 ( 2172) covalent geometry : bond 0.00346 (14382) covalent geometry : angle 0.59910 (19350) *********************** 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 282 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 210 time to evaluate : 1.734 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: 0.5215 (OUTLIER) cc_final: 0.4868 (t0) REVERT: A 364 LYS cc_start: 0.7684 (tttt) cc_final: 0.6777 (ttmt) REVERT: A 384 LEU cc_start: 0.7622 (tp) cc_final: 0.7334 (mm) REVERT: A 569 MET cc_start: 0.6525 (OUTLIER) cc_final: 0.4148 (mtt) REVERT: A 616 MET cc_start: 0.8407 (mmm) cc_final: 0.8178 (mmm) REVERT: A 626 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7505 (mm-30) REVERT: A 647 MET cc_start: 0.7223 (tpt) cc_final: 0.5278 (tpt) REVERT: A 687 TYR cc_start: 0.7118 (OUTLIER) cc_final: 0.5559 (t80) REVERT: A 738 LYS cc_start: 0.7517 (mmmm) cc_final: 0.7309 (mmmt) REVERT: A 921 PHE cc_start: 0.5889 (t80) cc_final: 0.5624 (t80) REVERT: A 950 ASP cc_start: 0.6809 (p0) cc_final: 0.6512 (p0) REVERT: A 1001 MET cc_start: 0.6027 (mmm) cc_final: 0.5580 (mmm) REVERT: B 585 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.7024 (tp) REVERT: B 624 GLU cc_start: 0.5902 (tp30) cc_final: 0.5660 (tp30) REVERT: B 713 ILE cc_start: 0.7058 (tp) cc_final: 0.6732 (tp) REVERT: B 763 LYS cc_start: 0.6547 (mptt) cc_final: 0.6326 (mptt) REVERT: B 765 ASN cc_start: 0.5008 (OUTLIER) cc_final: 0.4104 (p0) REVERT: B 976 MET cc_start: 0.5965 (tmm) cc_final: 0.5473 (tmm) REVERT: B 986 GLU cc_start: 0.7140 (pp20) cc_final: 0.6869 (pp20) REVERT: F 75 MET cc_start: 0.6819 (ptm) cc_final: 0.6483 (ptt) REVERT: F 176 ARG cc_start: 0.4694 (tmm160) cc_final: 0.4243 (tmm160) REVERT: F 231 MET cc_start: 0.2476 (pmm) cc_final: 0.1926 (pmm) outliers start: 72 outliers final: 50 residues processed: 260 average time/residue: 0.2668 time to fit residues: 104.0286 Evaluate side-chains 258 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 202 time to evaluate : 1.594 ------------------------------------------------------------------------------- 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 328 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 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 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 853 LEU Chi-restraints excluded: chain A residue 957 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 367 CYS Chi-restraints excluded: chain B residue 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 575 SER Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 740 LEU 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 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 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: 3.9990 chunk 101 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 81 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4772 r_free = 0.4772 target = 0.246459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.213002 restraints weight = 17175.679| |-----------------------------------------------------------------------------| r_work (start): 0.4468 rms_B_bonded: 2.19 r_work: 0.4337 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5972 moved from start: 0.3719 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= 0.131 Angle : 0.586 9.555 19350 Z= 0.311 Chirality : 0.041 0.302 2052 Planarity : 0.004 0.073 2480 Dihedral : 4.479 27.078 1858 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.56 % Allowed : 23.87 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.20), residues: 1682 helix: 0.83 (0.17), residues: 948 sheet: -1.29 (0.46), residues: 102 loop : -1.48 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 958 HIS 0.012 0.001 HIS B 852 PHE 0.028 0.001 PHE B 708 TYR 0.045 0.002 TYR A 625 ARG 0.005 0.000 ARG A 502 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 755) hydrogen bonds : angle 4.57692 ( 2172) covalent geometry : bond 0.00301 (14382) covalent geometry : angle 0.58586 (19350) *********************** 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 262 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 207 time to evaluate : 1.511 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: 0.5132 (OUTLIER) cc_final: 0.4905 (t0) REVERT: A 364 LYS cc_start: 0.7680 (tttt) cc_final: 0.6761 (ttmt) REVERT: A 384 LEU cc_start: 0.7621 (tp) cc_final: 0.7328 (mm) REVERT: A 569 MET cc_start: 0.6223 (OUTLIER) cc_final: 0.4998 (mpt) REVERT: A 616 MET cc_start: 0.8393 (mmm) cc_final: 0.8165 (mmm) REVERT: A 647 MET cc_start: 0.7195 (tpt) cc_final: 0.5288 (tpt) REVERT: A 687 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.5519 (t80) REVERT: A 921 PHE cc_start: 0.6007 (t80) cc_final: 0.5797 (t80) REVERT: A 930 MET cc_start: 0.5819 (mmm) cc_final: 0.5600 (tpt) REVERT: A 950 ASP cc_start: 0.6759 (p0) cc_final: 0.6489 (p0) REVERT: A 1001 MET cc_start: 0.5929 (mmm) cc_final: 0.5536 (mmm) REVERT: B 585 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6991 (tp) REVERT: B 624 GLU cc_start: 0.5811 (tp30) cc_final: 0.5464 (tp30) REVERT: B 713 ILE cc_start: 0.7002 (tp) cc_final: 0.6593 (tp) REVERT: B 763 LYS cc_start: 0.6511 (mptt) cc_final: 0.6197 (mptt) REVERT: B 765 ASN cc_start: 0.4962 (OUTLIER) cc_final: 0.2200 (t0) REVERT: B 964 ASP cc_start: 0.6564 (t0) cc_final: 0.5851 (m-30) REVERT: B 976 MET cc_start: 0.5947 (tmm) cc_final: 0.5430 (tmm) REVERT: B 986 GLU cc_start: 0.7047 (pp20) cc_final: 0.6793 (pp20) REVERT: F 51 TYR cc_start: 0.5297 (t80) cc_final: 0.4876 (t80) REVERT: F 75 MET cc_start: 0.6802 (ptm) cc_final: 0.6434 (ptt) REVERT: F 176 ARG cc_start: 0.4633 (tmm160) cc_final: 0.4247 (tmm160) REVERT: F 231 MET cc_start: 0.2492 (pmm) cc_final: 0.1934 (pmm) outliers start: 55 outliers final: 44 residues processed: 244 average time/residue: 0.2572 time to fit residues: 95.1940 Evaluate side-chains 249 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 1.707 ------------------------------------------------------------------------------- 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 328 ILE 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 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 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 575 SER 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 707 VAL Chi-restraints excluded: chain B residue 740 LEU 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 332 HIS B 852 HIS B 979 HIS F 34 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.244697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.210426 restraints weight = 17352.316| |-----------------------------------------------------------------------------| r_work (start): 0.4440 rms_B_bonded: 2.22 r_work: 0.4301 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14382 Z= 0.153 Angle : 0.619 10.602 19350 Z= 0.327 Chirality : 0.042 0.356 2052 Planarity : 0.004 0.074 2480 Dihedral : 4.557 26.980 1858 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.69 % Allowed : 23.48 % 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: -0.41 (0.20), residues: 1682 helix: 0.69 (0.16), residues: 955 sheet: -1.51 (0.44), residues: 112 loop : -1.51 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 958 HIS 0.012 0.001 HIS B 852 PHE 0.035 0.002 PHE B 708 TYR 0.049 0.002 TYR A 625 ARG 0.005 0.000 ARG A 480 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 755) hydrogen bonds : angle 4.63457 ( 2172) covalent geometry : bond 0.00357 (14382) covalent geometry : angle 0.61908 (19350) ********************** 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 265 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 208 time to evaluate : 1.485 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: 0.5006 (OUTLIER) cc_final: 0.4804 (t0) REVERT: A 364 LYS cc_start: 0.7679 (tttt) cc_final: 0.6741 (ttmt) REVERT: A 384 LEU cc_start: 0.7631 (tp) cc_final: 0.7372 (mm) REVERT: A 569 MET cc_start: 0.6408 (OUTLIER) cc_final: 0.4554 (mtt) REVERT: A 647 MET cc_start: 0.7248 (tpt) cc_final: 0.5412 (tpt) REVERT: A 687 TYR cc_start: 0.7128 (OUTLIER) cc_final: 0.5484 (t80) REVERT: A 722 PHE cc_start: 0.6445 (t80) cc_final: 0.6183 (t80) REVERT: A 921 PHE cc_start: 0.5872 (t80) cc_final: 0.5634 (t80) REVERT: A 950 ASP cc_start: 0.6847 (p0) cc_final: 0.6551 (p0) REVERT: A 1001 MET cc_start: 0.6032 (mmm) cc_final: 0.5652 (mmm) REVERT: B 713 ILE cc_start: 0.7087 (tp) cc_final: 0.6745 (tp) REVERT: B 763 LYS cc_start: 0.6606 (mptt) cc_final: 0.6287 (mptt) REVERT: B 765 ASN cc_start: 0.5063 (OUTLIER) cc_final: 0.4407 (p0) REVERT: B 930 MET cc_start: 0.1666 (mmm) cc_final: 0.1157 (tpt) REVERT: B 964 ASP cc_start: 0.6354 (t0) cc_final: 0.5835 (m-30) REVERT: B 986 GLU cc_start: 0.7148 (pp20) cc_final: 0.6878 (pp20) REVERT: F 51 TYR cc_start: 0.5307 (t80) cc_final: 0.4824 (t80) REVERT: F 75 MET cc_start: 0.6542 (ptm) cc_final: 0.6192 (ptt) REVERT: F 176 ARG cc_start: 0.4639 (tmm160) cc_final: 0.4272 (tmm160) outliers start: 57 outliers final: 45 residues processed: 245 average time/residue: 0.2588 time to fit residues: 95.0951 Evaluate side-chains 247 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 198 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 328 ILE 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 552 TYR Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 597 GLU Chi-restraints excluded: chain A residue 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 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 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 707 VAL Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 765 ASN Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 891 THR Chi-restraints excluded: chain B residue 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 67 PHE Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 221 GLU Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 235 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 85 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 83 optimal weight: 0.4980 chunk 5 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 90 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN A 895 ASN B 852 HIS B 979 HIS F 34 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.247454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.214233 restraints weight = 17329.763| |-----------------------------------------------------------------------------| r_work (start): 0.4481 rms_B_bonded: 2.20 r_work: 0.4355 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5941 moved from start: 0.4061 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= 0.128 Angle : 0.597 9.273 19350 Z= 0.317 Chirality : 0.042 0.310 2052 Planarity : 0.004 0.072 2480 Dihedral : 4.500 27.383 1858 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.23 % Allowed : 24.13 % 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: -0.35 (0.20), residues: 1682 helix: 0.76 (0.17), residues: 966 sheet: -1.39 (0.45), residues: 118 loop : -1.59 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 958 HIS 0.013 0.001 HIS B 852 PHE 0.037 0.002 PHE B 361 TYR 0.041 0.002 TYR A 611 ARG 0.011 0.000 ARG A 359 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 755) hydrogen bonds : angle 4.55989 ( 2172) covalent geometry : bond 0.00294 (14382) covalent geometry : angle 0.59741 (19350) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7061.76 seconds wall clock time: 125 minutes 6.77 seconds (7506.77 seconds total)