Starting phenix.real_space_refine on Wed Sep 17 18:20:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ga2_51169/09_2025/9ga2_51169.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ga2_51169/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ga2_51169/09_2025/9ga2_51169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ga2_51169/09_2025/9ga2_51169.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ga2_51169/09_2025/9ga2_51169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ga2_51169/09_2025/9ga2_51169.map" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.44, per 1000 atoms: 0.24 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: 0.96 Conformation dependent library (CDL) restraints added in 416.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.40 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: 1.25 Time building geometry restraints manager: 1.24 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 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: 5.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.850 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.790 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.23), 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 ARG 0.004 0.000 ARG A 835 TYR 0.014 0.001 TYR A 793 PHE 0.018 0.001 PHE A 47 TRP 0.009 0.002 TRP A 913 HIS 0.004 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00238 (10400) covalent geometry : angle 0.68385 (14094) hydrogen bonds : bond 0.15389 ( 417) hydrogen bonds : angle 7.44912 ( 1185) metal coordination : bond 0.05410 ( 10) metal coordination : angle 14.92044 ( 6) *********************** 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 : 0.478 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: 0.0741 time to fit residues: 7.7079 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 : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 886 ASN A 896 ASN ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 HIS B 567 HIS ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 ASN ** B 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.043460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.032725 restraints weight = 170224.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.032839 restraints weight = 159729.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.033029 restraints weight = 152941.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.033264 restraints weight = 146611.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.033261 restraints weight = 133636.946| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10410 Z= 0.222 Angle : 0.690 13.227 14100 Z= 0.355 Chirality : 0.045 0.158 1628 Planarity : 0.006 0.053 1854 Dihedral : 5.112 21.969 1482 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 30.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.18 % Allowed : 5.46 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.23), residues: 1331 helix: 0.08 (0.22), residues: 562 sheet: -0.29 (0.35), residues: 176 loop : -0.78 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 508 TYR 0.015 0.002 TYR A 54 PHE 0.013 0.002 PHE A 644 TRP 0.013 0.002 TRP B 913 HIS 0.006 0.002 HIS B 587 Details of bonding type rmsd covalent geometry : bond 0.00446 (10400) covalent geometry : angle 0.67018 (14094) hydrogen bonds : bond 0.04034 ( 417) hydrogen bonds : angle 6.50587 ( 1185) metal coordination : bond 0.01283 ( 10) metal coordination : angle 8.08644 ( 6) *********************** 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 48 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 46 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 766 MET cc_start: 0.4747 (tpt) cc_final: 0.4122 (tpt) REVERT: A 803 ASP cc_start: 0.9637 (t70) cc_final: 0.9293 (p0) outliers start: 2 outliers final: 0 residues processed: 48 average time/residue: 0.0784 time to fit residues: 6.3256 Evaluate side-chains 38 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 89 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 ** B 437 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 767 ASN B 820 HIS B 886 ASN ** 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 = 0.3127 r_free = 0.3127 target = 0.042722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.032093 restraints weight = 168867.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.032198 restraints weight = 157617.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.032198 restraints weight = 151375.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.032198 restraints weight = 151375.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.032198 restraints weight = 151375.995| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10410 Z= 0.181 Angle : 0.639 11.693 14100 Z= 0.327 Chirality : 0.044 0.152 1628 Planarity : 0.005 0.054 1854 Dihedral : 5.040 22.990 1482 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 26.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.23), residues: 1331 helix: 0.18 (0.22), residues: 550 sheet: -0.43 (0.35), residues: 176 loop : -0.88 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 547 TYR 0.015 0.002 TYR A 944 PHE 0.027 0.002 PHE A 768 TRP 0.008 0.002 TRP B 913 HIS 0.005 0.002 HIS B 877 Details of bonding type rmsd covalent geometry : bond 0.00376 (10400) covalent geometry : angle 0.62267 (14094) hydrogen bonds : bond 0.03654 ( 417) hydrogen bonds : angle 6.28268 ( 1185) metal coordination : bond 0.01059 ( 10) metal coordination : angle 6.92726 ( 6) *********************** 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 : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.7693 (p) cc_final: 0.7477 (m) REVERT: A 766 MET cc_start: 0.4669 (tpt) cc_final: 0.3798 (tpt) REVERT: A 803 ASP cc_start: 0.9667 (t70) cc_final: 0.9348 (p0) REVERT: B 69 MET cc_start: 0.6535 (ppp) cc_final: 0.6279 (ppp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0781 time to fit residues: 6.1555 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 : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 2 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS ** A 534 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 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 626 GLN ** 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 = 0.3015 r_free = 0.3015 target = 0.038940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.029261 restraints weight = 194621.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.029491 restraints weight = 176163.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.029614 restraints weight = 163030.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.029810 restraints weight = 154610.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.029827 restraints weight = 143501.671| |-----------------------------------------------------------------------------| r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 10410 Z= 0.324 Angle : 0.898 19.370 14100 Z= 0.464 Chirality : 0.051 0.217 1628 Planarity : 0.008 0.083 1854 Dihedral : 6.286 23.964 1482 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 47.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.27 % Allowed : 8.65 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.21), residues: 1331 helix: -0.81 (0.20), residues: 544 sheet: -1.11 (0.35), residues: 178 loop : -1.51 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG B 547 TYR 0.025 0.003 TYR A 944 PHE 0.022 0.003 PHE B 644 TRP 0.019 0.004 TRP B 913 HIS 0.015 0.003 HIS B 877 Details of bonding type rmsd covalent geometry : bond 0.00653 (10400) covalent geometry : angle 0.86904 (14094) hydrogen bonds : bond 0.04789 ( 417) hydrogen bonds : angle 7.07421 ( 1185) metal coordination : bond 0.01875 ( 10) metal coordination : angle 11.03217 ( 6) *********************** 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 38 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 766 MET cc_start: 0.4316 (tpt) cc_final: 0.3478 (tpt) REVERT: B 69 MET cc_start: 0.7195 (ppp) cc_final: 0.6850 (ppp) REVERT: B 278 PRO cc_start: 0.9633 (Cg_exo) cc_final: 0.9382 (Cg_endo) outliers start: 3 outliers final: 1 residues processed: 38 average time/residue: 0.0799 time to fit residues: 5.2395 Evaluate side-chains 28 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 45 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 48 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 437 HIS ** B 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 686 HIS B 896 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.040516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.028289 restraints weight = 181046.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.028800 restraints weight = 150134.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.029164 restraints weight = 130601.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.029387 restraints weight = 118071.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.029670 restraints weight = 110084.598| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5765 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10410 Z= 0.155 Angle : 0.657 14.742 14100 Z= 0.334 Chirality : 0.045 0.156 1628 Planarity : 0.005 0.048 1854 Dihedral : 5.505 23.768 1482 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 26.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.22), residues: 1331 helix: -0.25 (0.21), residues: 550 sheet: -1.08 (0.34), residues: 174 loop : -1.06 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 609 TYR 0.014 0.002 TYR A 944 PHE 0.013 0.002 PHE A 76 TRP 0.010 0.002 TRP A 913 HIS 0.007 0.002 HIS B 877 Details of bonding type rmsd covalent geometry : bond 0.00328 (10400) covalent geometry : angle 0.63534 (14094) hydrogen bonds : bond 0.03577 ( 417) hydrogen bonds : angle 6.28210 ( 1185) metal coordination : bond 0.01015 ( 10) metal coordination : angle 8.22388 ( 6) *********************** 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 42 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0813 time to fit residues: 5.7785 Evaluate side-chains 30 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 60 optimal weight: 0.0970 chunk 130 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 overall best weight: 4.6186 ------------------------------------------------------------------------------- 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 767 ASN ** A 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 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 = 0.2952 r_free = 0.2952 target = 0.038442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.026612 restraints weight = 188832.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.027071 restraints weight = 156707.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.027369 restraints weight = 135487.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.027604 restraints weight = 122486.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.027873 restraints weight = 114121.080| |-----------------------------------------------------------------------------| r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10410 Z= 0.245 Angle : 0.763 17.421 14100 Z= 0.392 Chirality : 0.047 0.164 1628 Planarity : 0.006 0.054 1854 Dihedral : 5.827 23.791 1482 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 37.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.22), residues: 1331 helix: -0.44 (0.21), residues: 545 sheet: -1.17 (0.36), residues: 160 loop : -1.33 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 508 TYR 0.016 0.002 TYR A 944 PHE 0.018 0.002 PHE B 878 TRP 0.009 0.003 TRP B 570 HIS 0.012 0.002 HIS B 877 Details of bonding type rmsd covalent geometry : bond 0.00501 (10400) covalent geometry : angle 0.73618 (14094) hydrogen bonds : bond 0.04129 ( 417) hydrogen bonds : angle 6.56191 ( 1185) metal coordination : bond 0.01311 ( 10) metal coordination : angle 9.81573 ( 6) *********************** 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 40 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0883 time to fit residues: 5.8080 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 : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 45 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 677 ASN ** B 681 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 = 0.2959 r_free = 0.2959 target = 0.038707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.026729 restraints weight = 184710.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.027217 restraints weight = 151939.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.027598 restraints weight = 131501.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.027805 restraints weight = 118370.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.028016 restraints weight = 110007.053| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5695 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10410 Z= 0.190 Angle : 0.695 15.666 14100 Z= 0.353 Chirality : 0.046 0.180 1628 Planarity : 0.005 0.067 1854 Dihedral : 5.630 24.118 1482 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 32.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.22), residues: 1331 helix: -0.19 (0.22), residues: 541 sheet: -1.13 (0.36), residues: 160 loop : -1.28 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 752 TYR 0.014 0.002 TYR A 61 PHE 0.013 0.002 PHE A 76 TRP 0.010 0.003 TRP B 570 HIS 0.009 0.002 HIS B 877 Details of bonding type rmsd covalent geometry : bond 0.00396 (10400) covalent geometry : angle 0.67122 (14094) hydrogen bonds : bond 0.03736 ( 417) hydrogen bonds : angle 6.33304 ( 1185) metal coordination : bond 0.00971 ( 10) metal coordination : angle 8.85309 ( 6) *********************** 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 39 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0964 time to fit residues: 6.0063 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 : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 76 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 69 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 103 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 112 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 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 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN ** A 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 GLN B 767 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.040977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.028577 restraints weight = 177035.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.029113 restraints weight = 147302.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.029474 restraints weight = 127701.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.029701 restraints weight = 115352.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.029882 restraints weight = 107698.419| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5740 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10410 Z= 0.111 Angle : 0.622 9.355 14100 Z= 0.309 Chirality : 0.045 0.152 1628 Planarity : 0.004 0.046 1854 Dihedral : 5.053 23.543 1482 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.23), residues: 1331 helix: 0.30 (0.22), residues: 530 sheet: -0.82 (0.36), residues: 166 loop : -0.87 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 752 TYR 0.013 0.001 TYR A 54 PHE 0.016 0.001 PHE A 76 TRP 0.014 0.003 TRP A 913 HIS 0.005 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00238 (10400) covalent geometry : angle 0.61339 (14094) hydrogen bonds : bond 0.03147 ( 417) hydrogen bonds : angle 5.74781 ( 1185) metal coordination : bond 0.00579 ( 10) metal coordination : angle 5.17463 ( 6) *********************** 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 43 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0933 time to fit residues: 6.4181 Evaluate side-chains 31 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 3 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 903 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.038540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.026904 restraints weight = 193357.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.027402 restraints weight = 159264.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.027621 restraints weight = 137137.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.028015 restraints weight = 126202.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.028254 restraints weight = 115488.376| |-----------------------------------------------------------------------------| r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5897 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10410 Z= 0.227 Angle : 0.702 12.827 14100 Z= 0.363 Chirality : 0.046 0.179 1628 Planarity : 0.006 0.046 1854 Dihedral : 5.440 23.987 1482 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 32.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.23), residues: 1331 helix: 0.06 (0.22), residues: 540 sheet: -1.18 (0.37), residues: 150 loop : -1.03 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 480 TYR 0.015 0.002 TYR A 113 PHE 0.013 0.002 PHE B 644 TRP 0.008 0.003 TRP B 570 HIS 0.011 0.002 HIS B 877 Details of bonding type rmsd covalent geometry : bond 0.00460 (10400) covalent geometry : angle 0.68575 (14094) hydrogen bonds : bond 0.03773 ( 417) hydrogen bonds : angle 6.19231 ( 1185) metal coordination : bond 0.01106 ( 10) metal coordination : angle 7.31411 ( 6) *********************** 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 38 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0794 time to fit residues: 5.2485 Evaluate side-chains 29 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 76 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- 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** B 458 ASN B 767 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.038212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.026752 restraints weight = 190881.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.027221 restraints weight = 157451.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.027614 restraints weight = 135870.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.027847 restraints weight = 122197.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.028133 restraints weight = 112070.610| |-----------------------------------------------------------------------------| r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10410 Z= 0.177 Angle : 0.668 13.640 14100 Z= 0.342 Chirality : 0.046 0.207 1628 Planarity : 0.005 0.046 1854 Dihedral : 5.469 25.506 1482 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 30.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.23), residues: 1331 helix: 0.03 (0.22), residues: 541 sheet: -1.25 (0.37), residues: 149 loop : -1.04 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 633 TYR 0.022 0.002 TYR A 113 PHE 0.020 0.002 PHE A 76 TRP 0.012 0.002 TRP A 913 HIS 0.018 0.002 HIS B 635 Details of bonding type rmsd covalent geometry : bond 0.00368 (10400) covalent geometry : angle 0.65121 (14094) hydrogen bonds : bond 0.03464 ( 417) hydrogen bonds : angle 6.17059 ( 1185) metal coordination : bond 0.00850 ( 10) metal coordination : angle 7.28976 ( 6) ********************** 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 40 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 LEU cc_start: 0.9670 (mm) cc_final: 0.9373 (tp) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0806 time to fit residues: 5.5604 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 : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 15 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 87 optimal weight: 0.0970 chunk 31 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 63 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 ** A 903 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 = 0.3070 r_free = 0.3070 target = 0.040195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.030089 restraints weight = 173674.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.030329 restraints weight = 160140.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.030522 restraints weight = 148409.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.030529 restraints weight = 134985.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.030529 restraints weight = 135544.654| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10410 Z= 0.112 Angle : 0.617 8.467 14100 Z= 0.309 Chirality : 0.045 0.175 1628 Planarity : 0.004 0.046 1854 Dihedral : 5.000 25.085 1482 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.23), residues: 1331 helix: 0.31 (0.22), residues: 540 sheet: -0.72 (0.38), residues: 151 loop : -0.78 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 786 TYR 0.016 0.002 TYR A 54 PHE 0.019 0.001 PHE A 76 TRP 0.015 0.003 TRP A 913 HIS 0.004 0.001 HIS A 587 Details of bonding type rmsd covalent geometry : bond 0.00236 (10400) covalent geometry : angle 0.61022 (14094) hydrogen bonds : bond 0.03035 ( 417) hydrogen bonds : angle 5.70790 ( 1185) metal coordination : bond 0.00526 ( 10) metal coordination : angle 4.52022 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1775.81 seconds wall clock time: 31 minutes 53.47 seconds (1913.47 seconds total)