Starting phenix.real_space_refine on Mon Jun 9 06:59:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ga2_51169/06_2025/9ga2_51169.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ga2_51169/06_2025/9ga2_51169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ga2_51169/06_2025/9ga2_51169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ga2_51169/06_2025/9ga2_51169.map" model { file = "/net/cci-nas-00/data/ceres_data/9ga2_51169/06_2025/9ga2_51169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ga2_51169/06_2025/9ga2_51169.cif" } resolution = 4.9 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= -0.000 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 22 5.16 5 C 6407 2.51 5 N 1836 2.21 5 O 1971 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10239 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5056 Classifications: {'peptide': 662} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 633} Chain breaks: 2 Chain: "B" Number of atoms: 5180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 5180 Classifications: {'peptide': 681} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 650} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3538 SG CYS A 753 27.423 56.766 17.602 1.00638.86 S ATOM 3711 SG CYS A 776 29.485 59.513 19.927 1.00832.41 S ATOM 3733 SG CYS A 779 27.485 56.122 21.146 1.00796.71 S ATOM 8718 SG CYS B 753 73.515 87.718 17.191 1.00385.23 S ATOM 8738 SG CYS B 756 71.064 90.099 18.613 1.00500.73 S ATOM 8891 SG CYS B 776 71.795 86.009 19.825 1.00496.62 S ATOM 8913 SG CYS B 779 73.775 88.892 20.559 1.00450.03 S ATOM 6086 SG CYS B 282 22.561 90.409 18.031 1.00640.58 S ATOM 6108 SG CYS B 285 26.513 91.364 19.367 1.00672.34 S ATOM 6136 SG CYS B 412 24.208 94.003 17.577 1.00703.62 S Time building chain proxies: 6.67, per 1000 atoms: 0.65 Number of scatterers: 10239 At special positions: 0 Unit cell: (99.568, 142.24, 75.565, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 22 16.00 O 1971 8.00 N 1836 7.00 C 6407 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: 2.53 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 779 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 776 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 753 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 756 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 776 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 753 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 779 " pdb=" ZN B1002 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 282 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 412 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 285 " Number of angles added : 6 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2404 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 10 sheets defined 46.6% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 37 through 57 removed outlier: 4.332A pdb=" N ALA A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 67 removed outlier: 3.620A pdb=" N ARG A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE A 65 " --> pdb=" O TYR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 104 through 117 removed outlier: 3.733A pdb=" N TYR A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 421 through 426 removed outlier: 3.615A pdb=" N LEU A 425 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 426 " --> pdb=" O PRO A 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 421 through 426' Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 463 through 487 removed outlier: 6.508A pdb=" N GLN A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL A 473 " --> pdb=" O ILE A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 518 removed outlier: 3.973A pdb=" N GLY A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 551 removed outlier: 4.093A pdb=" N ARG A 539 " --> pdb=" O GLN A 535 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG A 540 " --> pdb=" O ARG A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 568 Processing helix chain 'A' and resid 578 through 582 Processing helix chain 'A' and resid 590 through 597 Processing helix chain 'A' and resid 600 through 607 Processing helix chain 'A' and resid 659 through 667 Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 713 through 719 Processing helix chain 'A' and resid 719 through 730 removed outlier: 4.227A pdb=" N LYS A 723 " --> pdb=" O GLY A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 737 Processing helix chain 'A' and resid 740 through 745 Processing helix chain 'A' and resid 792 through 796 removed outlier: 4.001A pdb=" N GLY A 795 " --> pdb=" O HIS A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 804 Processing helix chain 'A' and resid 805 through 813 removed outlier: 4.421A pdb=" N GLU A 811 " --> pdb=" O GLU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 830 removed outlier: 3.844A pdb=" N TYR A 822 " --> pdb=" O GLY A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 843 Processing helix chain 'A' and resid 844 through 858 Processing helix chain 'A' and resid 877 through 893 Processing helix chain 'A' and resid 904 through 911 Processing helix chain 'A' and resid 933 through 940 Processing helix chain 'A' and resid 943 through 953 removed outlier: 3.833A pdb=" N GLU A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A 952 " --> pdb=" O PHE A 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 43 Processing helix chain 'B' and resid 46 through 57 removed outlier: 3.879A pdb=" N TYR B 54 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B 57 " --> pdb=" O ARG B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 98 through 104 removed outlier: 3.596A pdb=" N ILE B 102 " --> pdb=" O THR B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.548A pdb=" N TYR B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 427 Processing helix chain 'B' and resid 446 through 457 Processing helix chain 'B' and resid 458 through 462 removed outlier: 3.628A pdb=" N LEU B 462 " --> pdb=" O ALA B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 487 removed outlier: 5.730A pdb=" N GLN B 472 " --> pdb=" O ALA B 468 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL B 473 " --> pdb=" O ILE B 469 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 480 " --> pdb=" O GLU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 501 Processing helix chain 'B' and resid 502 through 518 removed outlier: 4.086A pdb=" N GLY B 518 " --> pdb=" O GLN B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 536 No H-bonds generated for 'chain 'B' and resid 534 through 536' Processing helix chain 'B' and resid 537 through 552 removed outlier: 3.723A pdb=" N LEU B 548 " --> pdb=" O THR B 544 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 568 Processing helix chain 'B' and resid 590 through 597 Processing helix chain 'B' and resid 600 through 608 Processing helix chain 'B' and resid 659 through 667 removed outlier: 3.788A pdb=" N VAL B 664 " --> pdb=" O LYS B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 677 Processing helix chain 'B' and resid 713 through 719 Processing helix chain 'B' and resid 719 through 730 removed outlier: 3.762A pdb=" N LYS B 723 " --> pdb=" O GLY B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 738 Processing helix chain 'B' and resid 740 through 745 Processing helix chain 'B' and resid 787 through 791 Processing helix chain 'B' and resid 797 through 804 removed outlier: 3.646A pdb=" N MET B 804 " --> pdb=" O GLU B 800 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 813 removed outlier: 4.316A pdb=" N GLU B 811 " --> pdb=" O GLU B 807 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 829 removed outlier: 4.151A pdb=" N TYR B 822 " --> pdb=" O GLY B 818 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 825 " --> pdb=" O ARG B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 843 Processing helix chain 'B' and resid 844 through 858 Processing helix chain 'B' and resid 877 through 894 removed outlier: 3.663A pdb=" N GLY B 890 " --> pdb=" O ASN B 886 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 891 " --> pdb=" O VAL B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 911 Processing helix chain 'B' and resid 933 through 940 Processing helix chain 'B' and resid 943 through 951 removed outlier: 3.975A pdb=" N GLU B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 10 removed outlier: 5.733A pdb=" N VAL A 18 " --> pdb=" O GLY A 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 86 removed outlier: 3.870A pdb=" N ASP A 527 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR A 524 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 558 " --> pdb=" O TYR A 524 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU A 526 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A 27 " --> pdb=" O TRP A 570 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N VAL A 572 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL A 29 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE A 574 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N THR A 31 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N HIS A 587 " --> pdb=" O ASP A 573 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 643 through 646 removed outlier: 6.430A pdb=" N ARG A 625 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 688 " --> pdb=" O VAL A 630 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 698 through 701 removed outlier: 6.750A pdb=" N VAL A 699 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ASP A 870 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N VAL A 701 " --> pdb=" O ASP A 870 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N TYR A 867 " --> pdb=" O ILE A 899 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ILE A 901 " --> pdb=" O TYR A 867 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU A 869 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 650 " --> pdb=" O VAL A 898 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 900 " --> pdb=" O THR A 650 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 915 " --> pdb=" O SER A 651 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 930 " --> pdb=" O ASP A 916 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY A 918 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL A 928 " --> pdb=" O GLY A 918 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 761 through 764 removed outlier: 3.945A pdb=" N ILE A 764 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL A 772 " --> pdb=" O ILE A 764 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 18 through 23 removed outlier: 5.538A pdb=" N VAL B 18 " --> pdb=" O GLY B 9 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 76 " --> pdb=" O LYS B 8 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 86 removed outlier: 4.177A pdb=" N ASP B 527 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU B 27 " --> pdb=" O TRP B 570 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL B 572 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL B 29 " --> pdb=" O VAL B 572 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 640 through 645 removed outlier: 6.096A pdb=" N ILE B 640 " --> pdb=" O GLY B 631 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY B 631 " --> pdb=" O ILE B 640 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 688 " --> pdb=" O VAL B 630 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 698 through 701 removed outlier: 4.242A pdb=" N ASP B 870 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TYR B 867 " --> pdb=" O ILE B 899 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ILE B 901 " --> pdb=" O TYR B 867 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU B 869 " --> pdb=" O ILE B 901 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 930 " --> pdb=" O ASP B 916 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLY B 918 " --> pdb=" O VAL B 928 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N VAL B 928 " --> pdb=" O GLY B 918 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 761 through 764 removed outlier: 3.965A pdb=" N VAL B 772 " --> pdb=" O ILE B 764 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1185 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: 3.75 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3539 1.34 - 1.46: 1903 1.46 - 1.58: 4930 1.58 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 10400 Sorted by residual: bond pdb=" CA GLU B 432 " pdb=" C GLU B 432 " ideal model delta sigma weight residual 1.521 1.532 -0.011 9.90e-03 1.02e+04 1.32e+00 bond pdb=" CA ILE B 816 " pdb=" CB ILE B 816 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.02e+00 bond pdb=" CA GLU A 528 " pdb=" C GLU A 528 " ideal model delta sigma weight residual 1.524 1.536 -0.012 1.26e-02 6.30e+03 9.62e-01 bond pdb=" CA LEU B 692 " pdb=" CB LEU B 692 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 8.88e-01 bond pdb=" N GLY B 431 " pdb=" CA GLY B 431 " ideal model delta sigma weight residual 1.458 1.449 0.009 9.20e-03 1.18e+04 8.82e-01 ... (remaining 10395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 13979 2.84 - 5.68: 98 5.68 - 8.52: 9 8.52 - 11.36: 5 11.36 - 14.21: 3 Bond angle restraints: 14094 Sorted by residual: angle pdb=" C HIS B 635 " pdb=" CA HIS B 635 " pdb=" CB HIS B 635 " ideal model delta sigma weight residual 116.54 109.70 6.84 1.15e+00 7.56e-01 3.53e+01 angle pdb=" CA LEU A 826 " pdb=" CB LEU A 826 " pdb=" CG LEU A 826 " ideal model delta sigma weight residual 116.30 130.51 -14.21 3.50e+00 8.16e-02 1.65e+01 angle pdb=" N LYS B 434 " pdb=" CA LYS B 434 " pdb=" C LYS B 434 " ideal model delta sigma weight residual 110.65 105.60 5.05 1.26e+00 6.30e-01 1.61e+01 angle pdb=" CA HIS B 635 " pdb=" C HIS B 635 " pdb=" N ASN B 636 " ideal model delta sigma weight residual 119.52 116.36 3.16 7.90e-01 1.60e+00 1.60e+01 angle pdb=" N THR B 428 " pdb=" CA THR B 428 " pdb=" C THR B 428 " ideal model delta sigma weight residual 108.45 113.28 -4.83 1.26e+00 6.30e-01 1.47e+01 ... (remaining 14089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.70: 5396 15.70 - 31.39: 664 31.39 - 47.09: 173 47.09 - 62.78: 25 62.78 - 78.48: 8 Dihedral angle restraints: 6266 sinusoidal: 2485 harmonic: 3781 Sorted by residual: dihedral pdb=" CA MET B 766 " pdb=" C MET B 766 " pdb=" N ASN B 767 " pdb=" CA ASN B 767 " ideal model delta harmonic sigma weight residual -180.00 -153.57 -26.43 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ASP A 75 " pdb=" C ASP A 75 " pdb=" N PHE A 76 " pdb=" CA PHE A 76 " ideal model delta harmonic sigma weight residual -180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA MET B 804 " pdb=" C MET B 804 " pdb=" N SER B 805 " pdb=" CA SER B 805 " ideal model delta harmonic sigma weight residual -180.00 -161.11 -18.89 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 6263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1458 0.074 - 0.147: 163 0.147 - 0.221: 3 0.221 - 0.294: 1 0.294 - 0.368: 3 Chirality restraints: 1628 Sorted by residual: chirality pdb=" CG LEU A 826 " pdb=" CB LEU A 826 " pdb=" CD1 LEU A 826 " pdb=" CD2 LEU A 826 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CG LEU B 826 " pdb=" CB LEU B 826 " pdb=" CD1 LEU B 826 " pdb=" CD2 LEU B 826 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CG LEU B 484 " pdb=" CB LEU B 484 " pdb=" CD1 LEU B 484 " pdb=" CD2 LEU B 484 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1625 not shown) Planarity restraints: 1854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 665 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C ASN A 665 " -0.039 2.00e-02 2.50e+03 pdb=" O ASN A 665 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP A 666 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 713 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO A 714 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 714 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 714 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 664 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C VAL B 664 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL B 664 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN B 665 " -0.011 2.00e-02 2.50e+03 ... (remaining 1851 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 5866 3.00 - 3.47: 12007 3.47 - 3.95: 18104 3.95 - 4.42: 21759 4.42 - 4.90: 31746 Nonbonded interactions: 89482 Sorted by model distance: nonbonded pdb=" O LEU A 448 " pdb=" OD1 ASP A 452 " model vdw 2.525 3.040 nonbonded pdb=" O TYR A 822 " pdb=" OG1 THR A 825 " model vdw 2.551 3.040 nonbonded pdb=" O SER A 449 " pdb=" OD1 ASP A 452 " model vdw 2.560 3.040 nonbonded pdb=" O SER B 799 " pdb=" OD1 ASP B 803 " model vdw 2.569 3.040 nonbonded pdb=" N ASP A 452 " pdb=" OD1 ASP A 452 " model vdw 2.577 3.120 ... (remaining 89477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 2 through 117 or resid 269 through 280 or resid 420 throug \ h 953 or resid 1001)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.070 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 : 0.003 0.156 10410 Z= 0.140 Angle : 0.750 31.536 14100 Z= 0.365 Chirality : 0.046 0.368 1628 Planarity : 0.004 0.048 1854 Dihedral : 14.548 78.479 3862 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.64 % Allowed : 16.48 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.08 (0.23), residues: 1331 helix: 0.43 (0.23), residues: 543 sheet: -0.21 (0.37), residues: 161 loop : -0.31 (0.26), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 913 HIS 0.004 0.001 HIS A 13 PHE 0.018 0.001 PHE A 47 TYR 0.014 0.001 TYR A 793 ARG 0.004 0.000 ARG A 835 Details of bonding type rmsd hydrogen bonds : bond 0.15389 ( 417) hydrogen bonds : angle 7.44912 ( 1185) metal coordination : bond 0.05410 ( 10) metal coordination : angle 14.92044 ( 6) covalent geometry : bond 0.00238 (10400) covalent geometry : angle 0.68385 (14094) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 766 MET cc_start: 0.2558 (tpt) cc_final: 0.1757 (tpt) REVERT: A 803 ASP cc_start: 0.9507 (t0) cc_final: 0.8954 (p0) REVERT: A 804 MET cc_start: 0.9203 (ppp) cc_final: 0.8912 (ppp) REVERT: A 857 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9247 (mt) REVERT: B 109 LEU cc_start: 0.9711 (OUTLIER) cc_final: 0.9374 (pp) REVERT: B 545 LEU cc_start: 0.9812 (mt) cc_final: 0.9566 (pp) REVERT: B 718 THR cc_start: 0.9405 (OUTLIER) cc_final: 0.9169 (p) outliers start: 18 outliers final: 13 residues processed: 59 average time/residue: 0.1516 time to fit residues: 15.7281 Evaluate side-chains 58 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 567 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 ASN ** A 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 HIS ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN ** B 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 792 HIS ** B 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 886 ASN ** B 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.040536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.030424 restraints weight = 179624.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.030526 restraints weight = 168136.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.030605 restraints weight = 160925.309| |-----------------------------------------------------------------------------| r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 10410 Z= 0.367 Angle : 0.926 18.142 14100 Z= 0.478 Chirality : 0.050 0.168 1628 Planarity : 0.008 0.080 1854 Dihedral : 5.978 23.688 1482 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 45.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.74 % Favored : 92.19 % Rotamer: Outliers : 0.55 % Allowed : 8.20 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.54 (0.21), residues: 1331 helix: -0.76 (0.20), residues: 562 sheet: -0.84 (0.34), residues: 173 loop : -1.20 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP B 913 HIS 0.010 0.002 HIS B 437 PHE 0.021 0.003 PHE A 644 TYR 0.022 0.003 TYR A 944 ARG 0.013 0.001 ARG B 680 Details of bonding type rmsd hydrogen bonds : bond 0.05108 ( 417) hydrogen bonds : angle 7.25605 ( 1185) metal coordination : bond 0.01682 ( 10) metal coordination : angle 11.17689 ( 6) covalent geometry : bond 0.00736 (10400) covalent geometry : angle 0.89723 (14094) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ILE cc_start: 0.9829 (mp) cc_final: 0.9555 (mm) REVERT: A 766 MET cc_start: 0.5291 (tpt) cc_final: 0.4712 (tpt) outliers start: 6 outliers final: 1 residues processed: 43 average time/residue: 0.1724 time to fit residues: 12.9213 Evaluate side-chains 32 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 48 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 HIS ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 HIS A 896 ASN ** A 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 HIS B 674 ASN ** B 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS B 767 ASN B 886 ASN ** B 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.042896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.032155 restraints weight = 167944.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.032383 restraints weight = 157846.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.032383 restraints weight = 145050.306| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10410 Z= 0.129 Angle : 0.620 10.096 14100 Z= 0.312 Chirality : 0.044 0.151 1628 Planarity : 0.005 0.048 1854 Dihedral : 5.099 23.123 1482 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.79 (0.22), residues: 1331 helix: 0.01 (0.22), residues: 560 sheet: -0.56 (0.35), residues: 176 loop : -0.93 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 913 HIS 0.004 0.001 HIS B 437 PHE 0.021 0.002 PHE A 768 TYR 0.015 0.002 TYR A 54 ARG 0.007 0.001 ARG B 547 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 417) hydrogen bonds : angle 6.23276 ( 1185) metal coordination : bond 0.00878 ( 10) metal coordination : angle 6.42154 ( 6) covalent geometry : bond 0.00276 (10400) covalent geometry : angle 0.60531 (14094) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 766 MET cc_start: 0.4581 (tpt) cc_final: 0.3668 (tpt) REVERT: B 69 MET cc_start: 0.6583 (ppp) cc_final: 0.6365 (ppp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1725 time to fit residues: 13.9249 Evaluate side-chains 36 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 65 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 115 optimal weight: 0.4980 chunk 43 optimal weight: 7.9990 chunk 16 optimal weight: 0.2980 chunk 96 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 ASN ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 GLN ** A 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 HIS ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN B 820 HIS ** B 896 ASN ** 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 = 0.3015 r_free = 0.3015 target = 0.040645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.028826 restraints weight = 182671.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.029280 restraints weight = 155270.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.029532 restraints weight = 136561.078| |-----------------------------------------------------------------------------| r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10410 Z= 0.217 Angle : 0.697 14.423 14100 Z= 0.358 Chirality : 0.046 0.162 1628 Planarity : 0.006 0.047 1854 Dihedral : 5.430 23.114 1482 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 34.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.08 (0.22), residues: 1331 helix: -0.09 (0.22), residues: 548 sheet: -0.89 (0.35), residues: 176 loop : -1.15 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP B 913 HIS 0.008 0.002 HIS B 877 PHE 0.012 0.002 PHE A 768 TYR 0.017 0.002 TYR A 944 ARG 0.008 0.001 ARG B 480 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 417) hydrogen bonds : angle 6.43019 ( 1185) metal coordination : bond 0.01339 ( 10) metal coordination : angle 8.32976 ( 6) covalent geometry : bond 0.00444 (10400) covalent geometry : angle 0.67536 (14094) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1694 time to fit residues: 12.2539 Evaluate side-chains 32 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 88 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 98 optimal weight: 0.0670 chunk 68 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 102 optimal weight: 0.0870 overall best weight: 2.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.041662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.031211 restraints weight = 168775.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.031211 restraints weight = 157064.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.031211 restraints weight = 157064.989| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10410 Z= 0.140 Angle : 0.612 11.873 14100 Z= 0.311 Chirality : 0.044 0.152 1628 Planarity : 0.005 0.048 1854 Dihedral : 5.133 23.396 1482 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 23.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.69 (0.23), residues: 1331 helix: 0.19 (0.22), residues: 548 sheet: -0.75 (0.34), residues: 176 loop : -0.88 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 570 HIS 0.005 0.001 HIS B 877 PHE 0.013 0.001 PHE A 76 TYR 0.020 0.002 TYR B 106 ARG 0.005 0.001 ARG A 609 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 417) hydrogen bonds : angle 6.04343 ( 1185) metal coordination : bond 0.00943 ( 10) metal coordination : angle 6.68689 ( 6) covalent geometry : bond 0.00297 (10400) covalent geometry : angle 0.59677 (14094) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.9614 (m-10) cc_final: 0.9400 (m-10) REVERT: A 766 MET cc_start: 0.3891 (tpt) cc_final: 0.3378 (tpt) REVERT: B 69 MET cc_start: 0.6310 (ppp) cc_final: 0.5961 (ppp) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1937 time to fit residues: 14.2074 Evaluate side-chains 36 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.041574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.031259 restraints weight = 169643.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.031423 restraints weight = 157362.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.031609 restraints weight = 149029.008| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10410 Z= 0.129 Angle : 0.597 10.294 14100 Z= 0.302 Chirality : 0.044 0.152 1628 Planarity : 0.004 0.049 1854 Dihedral : 4.920 23.319 1482 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 22.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.47 (0.23), residues: 1331 helix: 0.39 (0.22), residues: 542 sheet: -0.67 (0.35), residues: 166 loop : -0.74 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 570 HIS 0.006 0.001 HIS A 877 PHE 0.014 0.001 PHE A 76 TYR 0.014 0.001 TYR A 54 ARG 0.005 0.001 ARG B 480 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 417) hydrogen bonds : angle 5.81712 ( 1185) metal coordination : bond 0.00868 ( 10) metal coordination : angle 5.88318 ( 6) covalent geometry : bond 0.00274 (10400) covalent geometry : angle 0.58508 (14094) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.9607 (m-10) cc_final: 0.9398 (m-10) REVERT: A 766 MET cc_start: 0.3572 (tpt) cc_final: 0.2992 (tpt) REVERT: B 69 MET cc_start: 0.6014 (ppp) cc_final: 0.5604 (ppp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1711 time to fit residues: 13.1486 Evaluate side-chains 36 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 117 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN ** A 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 ASN ** 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 = 0.3038 r_free = 0.3038 target = 0.041356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.028913 restraints weight = 179549.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.029433 restraints weight = 148040.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 14)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.029770 restraints weight = 128468.625| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5619 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10410 Z= 0.134 Angle : 0.596 10.107 14100 Z= 0.303 Chirality : 0.043 0.151 1628 Planarity : 0.005 0.048 1854 Dihedral : 4.901 23.249 1482 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.09 % Allowed : 1.64 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.42 (0.23), residues: 1331 helix: 0.43 (0.22), residues: 542 sheet: -0.62 (0.35), residues: 166 loop : -0.72 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 570 HIS 0.008 0.001 HIS A 877 PHE 0.014 0.001 PHE A 76 TYR 0.013 0.001 TYR A 54 ARG 0.007 0.001 ARG A 688 Details of bonding type rmsd hydrogen bonds : bond 0.03236 ( 417) hydrogen bonds : angle 5.74013 ( 1185) metal coordination : bond 0.00872 ( 10) metal coordination : angle 5.75039 ( 6) covalent geometry : bond 0.00286 (10400) covalent geometry : angle 0.58387 (14094) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.2255 time to fit residues: 16.3057 Evaluate side-chains 36 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 125 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 107 optimal weight: 0.2980 chunk 131 optimal weight: 30.0000 chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 889 ASN ** A 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 ASN ** 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 = 0.3053 r_free = 0.3053 target = 0.041669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.029170 restraints weight = 175730.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.029708 restraints weight = 146529.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.030049 restraints weight = 127674.639| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5653 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10410 Z= 0.115 Angle : 0.580 8.620 14100 Z= 0.292 Chirality : 0.043 0.151 1628 Planarity : 0.004 0.049 1854 Dihedral : 4.742 23.221 1482 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.23), residues: 1331 helix: 0.52 (0.23), residues: 535 sheet: -0.48 (0.36), residues: 166 loop : -0.66 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 570 HIS 0.004 0.001 HIS B 877 PHE 0.014 0.001 PHE A 76 TYR 0.013 0.001 TYR A 54 ARG 0.008 0.001 ARG A 508 Details of bonding type rmsd hydrogen bonds : bond 0.02992 ( 417) hydrogen bonds : angle 5.58724 ( 1185) metal coordination : bond 0.00726 ( 10) metal coordination : angle 4.83033 ( 6) covalent geometry : bond 0.00245 (10400) covalent geometry : angle 0.57171 (14094) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.2135 time to fit residues: 15.2599 Evaluate side-chains 33 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 124 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 133 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 GLN A 767 ASN ** A 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 ASN ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 ASN ** 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 = 0.3095 r_free = 0.3095 target = 0.041731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.031313 restraints weight = 169649.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.031575 restraints weight = 155807.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.031823 restraints weight = 141921.275| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10410 Z= 0.111 Angle : 0.583 9.762 14100 Z= 0.290 Chirality : 0.043 0.150 1628 Planarity : 0.004 0.049 1854 Dihedral : 4.674 23.073 1482 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.16 (0.23), residues: 1331 helix: 0.65 (0.23), residues: 534 sheet: -0.39 (0.36), residues: 166 loop : -0.60 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 570 HIS 0.004 0.001 HIS B 877 PHE 0.014 0.001 PHE A 76 TYR 0.013 0.001 TYR A 54 ARG 0.004 0.000 ARG B 480 Details of bonding type rmsd hydrogen bonds : bond 0.02960 ( 417) hydrogen bonds : angle 5.58125 ( 1185) metal coordination : bond 0.00720 ( 10) metal coordination : angle 4.51577 ( 6) covalent geometry : bond 0.00240 (10400) covalent geometry : angle 0.57589 (14094) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.9628 (m-10) cc_final: 0.9366 (m-10) REVERT: A 766 MET cc_start: 0.3265 (tpt) cc_final: 0.2692 (tpt) REVERT: A 803 ASP cc_start: 0.9662 (t70) cc_final: 0.9327 (p0) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.2068 time to fit residues: 14.4972 Evaluate side-chains 34 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 48 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.1980 chunk 98 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 96 optimal weight: 0.4980 chunk 8 optimal weight: 8.9990 chunk 56 optimal weight: 0.3980 chunk 33 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 GLN B 767 ASN B 896 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.042465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.031898 restraints weight = 165399.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.032172 restraints weight = 153080.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.032417 restraints weight = 138980.108| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10410 Z= 0.100 Angle : 0.589 9.087 14100 Z= 0.286 Chirality : 0.044 0.160 1628 Planarity : 0.004 0.049 1854 Dihedral : 4.521 22.975 1482 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.09 % Allowed : 0.73 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.02 (0.24), residues: 1331 helix: 0.69 (0.23), residues: 536 sheet: -0.16 (0.38), residues: 160 loop : -0.50 (0.27), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 570 HIS 0.006 0.001 HIS A 437 PHE 0.011 0.001 PHE B 47 TYR 0.013 0.001 TYR A 106 ARG 0.004 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.02966 ( 417) hydrogen bonds : angle 5.35918 ( 1185) metal coordination : bond 0.00534 ( 10) metal coordination : angle 3.46218 ( 6) covalent geometry : bond 0.00214 (10400) covalent geometry : angle 0.58440 (14094) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2662 Ramachandran restraints generated. 1331 Oldfield, 0 Emsley, 1331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 766 MET cc_start: 0.4039 (tpt) cc_final: 0.3572 (tpt) REVERT: A 803 ASP cc_start: 0.9664 (t70) cc_final: 0.9362 (p0) REVERT: B 526 LEU cc_start: 0.9414 (mm) cc_final: 0.8767 (tp) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.1695 time to fit residues: 12.9620 Evaluate side-chains 35 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 102 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 45 optimal weight: 0.2980 chunk 133 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 13 optimal weight: 0.2980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.042331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.031759 restraints weight = 165699.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.032036 restraints weight = 153731.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.032042 restraints weight = 138612.260| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10410 Z= 0.100 Angle : 0.566 8.345 14100 Z= 0.278 Chirality : 0.043 0.150 1628 Planarity : 0.004 0.048 1854 Dihedral : 4.445 22.270 1482 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.09 % Allowed : 0.27 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.05 (0.24), residues: 1331 helix: 0.77 (0.23), residues: 535 sheet: -0.04 (0.38), residues: 162 loop : -0.50 (0.27), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 570 HIS 0.004 0.001 HIS A 437 PHE 0.017 0.001 PHE A 76 TYR 0.019 0.001 TYR A 54 ARG 0.004 0.000 ARG B 688 Details of bonding type rmsd hydrogen bonds : bond 0.02805 ( 417) hydrogen bonds : angle 5.33812 ( 1185) metal coordination : bond 0.00610 ( 10) metal coordination : angle 3.34197 ( 6) covalent geometry : bond 0.00217 (10400) covalent geometry : angle 0.56167 (14094) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3206.32 seconds wall clock time: 58 minutes 35.21 seconds (3515.21 seconds total)