Starting phenix.real_space_refine on Sun Dec 29 16:33:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8clk_16715/12_2024/8clk_16715.cif Found real_map, /net/cci-nas-00/data/ceres_data/8clk_16715/12_2024/8clk_16715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8clk_16715/12_2024/8clk_16715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8clk_16715/12_2024/8clk_16715.map" model { file = "/net/cci-nas-00/data/ceres_data/8clk_16715/12_2024/8clk_16715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8clk_16715/12_2024/8clk_16715.cif" } resolution = 3.5 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= 0.005 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 6885 2.51 5 N 1856 2.21 5 O 1986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10799 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4899 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 31, 'TRANS': 579} Chain breaks: 3 Chain: "D" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3667 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 444} Chain breaks: 2 Chain: "E" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1421 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 14, 'TRANS': 159} Chain breaks: 1 Chain: "F" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 812 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 2 Time building chain proxies: 7.54, per 1000 atoms: 0.70 Number of scatterers: 10799 At special positions: 0 Unit cell: (105.216, 114.258, 155.358, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1986 8.00 N 1856 7.00 C 6885 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: 2.85 Conformation dependent library (CDL) restraints added in 2.0 seconds 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2558 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 8 sheets defined 54.7% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 1266 through 1284 Processing helix chain 'A' and resid 1294 through 1305 Processing helix chain 'A' and resid 1306 through 1311 Processing helix chain 'A' and resid 1312 through 1323 removed outlier: 4.208A pdb=" N ARG A1321 " --> pdb=" O GLY A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1326 through 1342 Processing helix chain 'A' and resid 1343 through 1346 removed outlier: 3.738A pdb=" N LEU A1346 " --> pdb=" O ASP A1343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1343 through 1346' Processing helix chain 'A' and resid 1347 through 1352 Processing helix chain 'A' and resid 1359 through 1378 removed outlier: 3.794A pdb=" N GLU A1376 " --> pdb=" O GLU A1372 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A1377 " --> pdb=" O LYS A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1399 Processing helix chain 'A' and resid 1420 through 1438 removed outlier: 5.072A pdb=" N ASN A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN A1434 " --> pdb=" O GLN A1430 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A1438 " --> pdb=" O GLN A1434 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1447 Processing helix chain 'A' and resid 1448 through 1457 removed outlier: 3.653A pdb=" N LEU A1455 " --> pdb=" O GLN A1451 " (cutoff:3.500A) Processing helix chain 'A' and resid 1460 through 1474 Processing helix chain 'A' and resid 1504 through 1512 removed outlier: 3.527A pdb=" N PHE A1511 " --> pdb=" O TYR A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1531 Processing helix chain 'A' and resid 1546 through 1548 No H-bonds generated for 'chain 'A' and resid 1546 through 1548' Processing helix chain 'A' and resid 1565 through 1578 removed outlier: 3.979A pdb=" N VAL A1571 " --> pdb=" O ASN A1567 " (cutoff:3.500A) Processing helix chain 'A' and resid 1694 through 1698 removed outlier: 3.706A pdb=" N LEU A1698 " --> pdb=" O LEU A1695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1701 through 1705 Processing helix chain 'A' and resid 1706 through 1710 Processing helix chain 'A' and resid 1714 through 1718 removed outlier: 4.175A pdb=" N ASN A1718 " --> pdb=" O PRO A1715 " (cutoff:3.500A) Processing helix chain 'A' and resid 1721 through 1732 removed outlier: 4.124A pdb=" N PHE A1725 " --> pdb=" O SER A1721 " (cutoff:3.500A) Processing helix chain 'A' and resid 1735 through 1752 removed outlier: 3.865A pdb=" N ALA A1748 " --> pdb=" O GLU A1744 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A1749 " --> pdb=" O ILE A1745 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR A1752 " --> pdb=" O ALA A1748 " (cutoff:3.500A) Processing helix chain 'A' and resid 1759 through 1766 Processing helix chain 'A' and resid 1767 through 1770 Processing helix chain 'A' and resid 1779 through 1790 Processing helix chain 'A' and resid 1807 through 1811 removed outlier: 5.643A pdb=" N TRP A1810 " --> pdb=" O GLY A1807 " (cutoff:3.500A) Proline residue: A1811 - end of helix No H-bonds generated for 'chain 'A' and resid 1807 through 1811' Processing helix chain 'A' and resid 1996 through 1999 Processing helix chain 'A' and resid 2000 through 2013 Processing helix chain 'A' and resid 2017 through 2025 removed outlier: 3.947A pdb=" N ARG A2023 " --> pdb=" O SER A2019 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR A2025 " --> pdb=" O LEU A2021 " (cutoff:3.500A) Processing helix chain 'A' and resid 2030 through 2044 removed outlier: 3.652A pdb=" N VAL A2034 " --> pdb=" O GLN A2030 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A2035 " --> pdb=" O PRO A2031 " (cutoff:3.500A) Processing helix chain 'A' and resid 2088 through 2095 Processing helix chain 'A' and resid 2102 through 2108 removed outlier: 4.236A pdb=" N LYS A2105 " --> pdb=" O ASN A2102 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP A2106 " --> pdb=" O TRP A2103 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N HIS A2108 " --> pdb=" O LYS A2105 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 433 Processing helix chain 'D' and resid 439 through 448 Processing helix chain 'D' and resid 457 through 469 Processing helix chain 'D' and resid 471 through 486 Processing helix chain 'D' and resid 489 through 504 removed outlier: 3.523A pdb=" N SER D 497 " --> pdb=" O ARG D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 547 removed outlier: 6.596A pdb=" N ASN D 527 " --> pdb=" O ALA D 523 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA D 528 " --> pdb=" O GLN D 524 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN D 530 " --> pdb=" O ALA D 526 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN D 531 " --> pdb=" O ASN D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 569 removed outlier: 6.335A pdb=" N VAL D 566 " --> pdb=" O MET D 562 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA D 567 " --> pdb=" O LEU D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 582 Processing helix chain 'D' and resid 604 through 606 No H-bonds generated for 'chain 'D' and resid 604 through 606' Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.657A pdb=" N VAL D 619 " --> pdb=" O VAL D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 621 through 639 Processing helix chain 'D' and resid 641 through 655 Processing helix chain 'D' and resid 655 through 660 Processing helix chain 'D' and resid 661 through 679 Processing helix chain 'D' and resid 681 through 696 removed outlier: 3.564A pdb=" N ASN D 687 " --> pdb=" O ARG D 683 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR D 688 " --> pdb=" O LYS D 684 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 713 removed outlier: 3.563A pdb=" N TRP D 703 " --> pdb=" O LYS D 699 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE D 705 " --> pdb=" O GLN D 701 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN D 708 " --> pdb=" O ASN D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 729 removed outlier: 3.568A pdb=" N PHE D 721 " --> pdb=" O ARG D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 746 removed outlier: 3.580A pdb=" N GLY D 740 " --> pdb=" O CYS D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 763 removed outlier: 4.099A pdb=" N GLY D 754 " --> pdb=" O LYS D 750 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN D 755 " --> pdb=" O HIS D 751 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR D 762 " --> pdb=" O GLN D 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 783 removed outlier: 3.844A pdb=" N ILE D 778 " --> pdb=" O GLY D 774 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN D 783 " --> pdb=" O HIS D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 808 removed outlier: 3.593A pdb=" N LEU D 792 " --> pdb=" O ARG D 788 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE D 799 " --> pdb=" O GLN D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 824 removed outlier: 3.739A pdb=" N LEU D 824 " --> pdb=" O GLY D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 826 through 840 removed outlier: 4.958A pdb=" N HIS D 832 " --> pdb=" O HIS D 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 854 Processing helix chain 'D' and resid 855 through 870 Processing helix chain 'D' and resid 872 through 884 Processing helix chain 'E' and resid 35 through 43 Proline residue: E 41 - end of helix Processing helix chain 'E' and resid 44 through 54 Processing helix chain 'F' and resid 34 through 39 Processing sheet with id=AA1, first strand: chain 'A' and resid 1400 through 1405 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1400 through 1405 current: chain 'E' and resid 74 through 95 removed outlier: 7.305A pdb=" N CYS E 75 " --> pdb=" O GLN E 124 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN E 124 " --> pdb=" O CYS E 75 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER E 118 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER E 83 " --> pdb=" O ILE E 116 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ILE E 116 " --> pdb=" O SER E 83 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU E 85 " --> pdb=" O LEU E 114 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 104 through 125 current: chain 'F' and resid 54 through 57 removed outlier: 5.487A pdb=" N VAL F 61 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU F 65 " --> pdb=" O SER F 104 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N MET F 100 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 11.874A pdb=" N GLY F 71 " --> pdb=" O HIS F 98 " (cutoff:3.500A) removed outlier: 10.196A pdb=" N HIS F 98 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 11.698A pdb=" N CYS F 73 " --> pdb=" O LYS F 96 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N LYS F 96 " --> pdb=" O CYS F 73 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE F 75 " --> pdb=" O LYS F 94 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LYS F 94 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLU F 77 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL F 92 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN F 79 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LYS F 90 " --> pdb=" O ASN F 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1477 through 1479 Processing sheet with id=AA3, first strand: chain 'A' and resid 1535 through 1536 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1535 through 1536 current: chain 'A' and resid 1675 through 1680 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1757 through 1758 Processing sheet with id=AA5, first strand: chain 'A' and resid 1813 through 1818 Processing sheet with id=AA6, first strand: chain 'A' and resid 2068 through 2069 removed outlier: 4.132A pdb=" N TRP A2051 " --> pdb=" O VAL A2069 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 573 through 578 Processing sheet with id=AA8, first strand: chain 'E' and resid 134 through 136 501 hydrogen bonds defined for protein. 1446 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: 3.30 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3538 1.34 - 1.46: 1564 1.46 - 1.57: 5809 1.57 - 1.69: 0 1.69 - 1.81: 109 Bond restraints: 11020 Sorted by residual: bond pdb=" CG LEU F 24 " pdb=" CD1 LEU F 24 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" CG1 ILE E 117 " pdb=" CD1 ILE E 117 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.91e+00 bond pdb=" CG1 ILE A2010 " pdb=" CD1 ILE A2010 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.69e+00 bond pdb=" CG1 ILE D 859 " pdb=" CD1 ILE D 859 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.64e+00 bond pdb=" CA ALA E 133 " pdb=" C ALA E 133 " ideal model delta sigma weight residual 1.531 1.517 0.014 1.12e-02 7.97e+03 1.64e+00 ... (remaining 11015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 13640 1.26 - 2.53: 1033 2.53 - 3.79: 184 3.79 - 5.06: 40 5.06 - 6.32: 5 Bond angle restraints: 14902 Sorted by residual: angle pdb=" C CYS A1673 " pdb=" N GLN A1674 " pdb=" CA GLN A1674 " ideal model delta sigma weight residual 120.75 125.07 -4.32 1.51e+00 4.39e-01 8.17e+00 angle pdb=" N CYS A1673 " pdb=" CA CYS A1673 " pdb=" C CYS A1673 " ideal model delta sigma weight residual 109.24 113.82 -4.58 1.67e+00 3.59e-01 7.52e+00 angle pdb=" C ILE A1519 " pdb=" CA ILE A1519 " pdb=" CB ILE A1519 " ideal model delta sigma weight residual 111.88 108.42 3.46 1.28e+00 6.10e-01 7.29e+00 angle pdb=" N THR A1518 " pdb=" CA THR A1518 " pdb=" C THR A1518 " ideal model delta sigma weight residual 111.71 114.63 -2.92 1.15e+00 7.56e-01 6.46e+00 angle pdb=" N CYS A2089 " pdb=" CA CYS A2089 " pdb=" C CYS A2089 " ideal model delta sigma weight residual 111.33 114.30 -2.97 1.21e+00 6.83e-01 6.03e+00 ... (remaining 14897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 6168 17.86 - 35.72: 432 35.72 - 53.58: 62 53.58 - 71.45: 19 71.45 - 89.31: 10 Dihedral angle restraints: 6691 sinusoidal: 2747 harmonic: 3944 Sorted by residual: dihedral pdb=" CA TYR A1400 " pdb=" C TYR A1400 " pdb=" N ARG A1401 " pdb=" CA ARG A1401 " ideal model delta harmonic sigma weight residual 180.00 151.18 28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA LYS A2000 " pdb=" C LYS A2000 " pdb=" N GLY A2001 " pdb=" CA GLY A2001 " ideal model delta harmonic sigma weight residual 180.00 152.06 27.94 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA LEU F 70 " pdb=" C LEU F 70 " pdb=" N GLY F 71 " pdb=" CA GLY F 71 " ideal model delta harmonic sigma weight residual 180.00 152.11 27.89 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 6688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 963 0.033 - 0.067: 458 0.067 - 0.100: 165 0.100 - 0.133: 71 0.133 - 0.166: 13 Chirality restraints: 1670 Sorted by residual: chirality pdb=" CA ARG E 185 " pdb=" N ARG E 185 " pdb=" C ARG E 185 " pdb=" CB ARG E 185 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA VAL F 45 " pdb=" N VAL F 45 " pdb=" C VAL F 45 " pdb=" CB VAL F 45 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" CB ILE A1519 " pdb=" CA ILE A1519 " pdb=" CG1 ILE A1519 " pdb=" CG2 ILE A1519 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 1667 not shown) Planarity restraints: 1909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 22 " -0.272 9.50e-02 1.11e+02 1.23e-01 1.14e+01 pdb=" NE ARG E 22 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG E 22 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG E 22 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG E 22 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 65 " -0.241 9.50e-02 1.11e+02 1.09e-01 9.18e+00 pdb=" NE ARG E 65 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG E 65 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG E 65 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG E 65 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1776 " -0.211 9.50e-02 1.11e+02 9.54e-02 7.35e+00 pdb=" NE ARG A1776 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A1776 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG A1776 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A1776 " 0.000 2.00e-02 2.50e+03 ... (remaining 1906 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1379 2.75 - 3.29: 11684 3.29 - 3.83: 17733 3.83 - 4.36: 21907 4.36 - 4.90: 36328 Nonbonded interactions: 89031 Sorted by model distance: nonbonded pdb=" NH2 ARG E 65 " pdb=" OD2 ASP E 68 " model vdw 2.217 3.120 nonbonded pdb=" NZ LYS A1535 " pdb=" O ARG A1680 " model vdw 2.258 3.120 nonbonded pdb=" O PHE A1544 " pdb=" NH1 ARG A1585 " model vdw 2.284 3.120 nonbonded pdb=" O ILE F 48 " pdb=" OH TYR F 66 " model vdw 2.285 3.040 nonbonded pdb=" O GLU A1388 " pdb=" OH TYR A1400 " model vdw 2.299 3.040 ... (remaining 89026 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.630 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.430 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11020 Z= 0.334 Angle : 0.754 6.321 14902 Z= 0.429 Chirality : 0.047 0.166 1670 Planarity : 0.009 0.123 1909 Dihedral : 13.293 89.307 4133 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -1.42 (0.21), residues: 1320 helix: -1.12 (0.17), residues: 639 sheet: -0.30 (0.45), residues: 110 loop : -0.63 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A1987 HIS 0.007 0.001 HIS A2024 PHE 0.035 0.003 PHE D 744 TYR 0.027 0.005 TYR D 756 ARG 0.026 0.003 ARG E 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1269 GLU cc_start: 0.8615 (mp0) cc_final: 0.8216 (mp0) REVERT: A 1270 ASP cc_start: 0.8213 (m-30) cc_final: 0.7686 (m-30) REVERT: A 1305 PHE cc_start: 0.8302 (m-80) cc_final: 0.8022 (m-80) REVERT: A 1330 TYR cc_start: 0.8230 (t80) cc_final: 0.7943 (t80) REVERT: A 1341 TYR cc_start: 0.8088 (t80) cc_final: 0.7860 (t80) REVERT: A 1530 MET cc_start: 0.6565 (tpp) cc_final: 0.6207 (mmm) REVERT: A 1545 LYS cc_start: 0.7992 (tttt) cc_final: 0.7750 (mmtm) REVERT: A 1729 LEU cc_start: 0.9110 (mp) cc_final: 0.8807 (mt) REVERT: A 1734 TYR cc_start: 0.6727 (m-80) cc_final: 0.6369 (m-80) REVERT: A 1760 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6584 (tp30) REVERT: A 1769 LEU cc_start: 0.7802 (mt) cc_final: 0.7588 (tp) REVERT: D 564 LEU cc_start: 0.9195 (mt) cc_final: 0.8944 (mm) REVERT: D 568 MET cc_start: 0.9545 (mtp) cc_final: 0.9151 (mpp) REVERT: D 667 GLU cc_start: 0.8803 (tp30) cc_final: 0.8124 (tp30) REVERT: D 736 CYS cc_start: 0.8437 (t) cc_final: 0.8080 (m) REVERT: D 850 LEU cc_start: 0.6575 (tp) cc_final: 0.6302 (mt) REVERT: F 34 ASP cc_start: 0.7749 (t0) cc_final: 0.7298 (t0) REVERT: F 106 THR cc_start: 0.9244 (m) cc_final: 0.8957 (p) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.3225 time to fit residues: 109.7853 Evaluate side-chains 161 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 0.0010 chunk 67 optimal weight: 50.0000 chunk 53 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1431 ASN ** A1478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1505 GLN D 739 ASN D 823 GLN E 162 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11020 Z= 0.229 Angle : 0.689 9.684 14902 Z= 0.360 Chirality : 0.044 0.398 1670 Planarity : 0.005 0.055 1909 Dihedral : 5.891 25.850 1473 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.92 % Allowed : 7.70 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.23), residues: 1320 helix: 0.17 (0.19), residues: 654 sheet: -0.60 (0.43), residues: 122 loop : -0.16 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 625 HIS 0.010 0.001 HIS E 135 PHE 0.024 0.003 PHE A1453 TYR 0.020 0.002 TYR D 655 ARG 0.011 0.001 ARG A1529 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1269 GLU cc_start: 0.8598 (mp0) cc_final: 0.8312 (mp0) REVERT: A 1305 PHE cc_start: 0.8261 (m-80) cc_final: 0.7714 (m-80) REVERT: A 1341 TYR cc_start: 0.8040 (t80) cc_final: 0.7793 (t80) REVERT: A 1453 PHE cc_start: 0.7555 (t80) cc_final: 0.7032 (t80) REVERT: A 1528 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7453 (m-30) REVERT: A 1545 LYS cc_start: 0.7816 (tttt) cc_final: 0.7482 (mptt) REVERT: A 1597 MET cc_start: 0.6271 (pmm) cc_final: 0.5973 (pmm) REVERT: A 1729 LEU cc_start: 0.9083 (mp) cc_final: 0.8774 (mt) REVERT: A 1734 TYR cc_start: 0.6750 (m-80) cc_final: 0.6471 (m-80) REVERT: A 1806 MET cc_start: 0.7989 (mmm) cc_final: 0.6799 (mmm) REVERT: A 2080 MET cc_start: 0.6967 (ttt) cc_final: 0.6637 (ttt) REVERT: D 472 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.7828 (mmm) REVERT: D 555 THR cc_start: 0.9476 (p) cc_final: 0.9047 (t) REVERT: D 556 LEU cc_start: 0.9568 (mt) cc_final: 0.9175 (mt) REVERT: D 568 MET cc_start: 0.9326 (mtp) cc_final: 0.8982 (mtt) REVERT: D 570 ARG cc_start: 0.8605 (mmm160) cc_final: 0.8383 (mmm160) REVERT: D 736 CYS cc_start: 0.8330 (t) cc_final: 0.8078 (m) REVERT: D 739 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.8123 (m-40) REVERT: D 795 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8090 (mp10) REVERT: D 850 LEU cc_start: 0.6340 (tp) cc_final: 0.6140 (mt) REVERT: E 135 HIS cc_start: 0.6708 (t-170) cc_final: 0.6471 (t-170) REVERT: E 145 MET cc_start: 0.8347 (mpp) cc_final: 0.7891 (mpp) REVERT: F 19 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7006 (pt0) REVERT: F 106 THR cc_start: 0.9002 (m) cc_final: 0.8650 (p) outliers start: 23 outliers final: 13 residues processed: 195 average time/residue: 0.2614 time to fit residues: 71.3366 Evaluate side-chains 164 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1314 HIS Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1499 MET Chi-restraints excluded: chain A residue 1528 ASP Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1710 THR Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1744 GLU Chi-restraints excluded: chain D residue 472 MET Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 739 ASN Chi-restraints excluded: chain D residue 795 GLN Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 123 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1567 ASN ** A2030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11020 Z= 0.228 Angle : 0.671 13.200 14902 Z= 0.341 Chirality : 0.044 0.336 1670 Planarity : 0.004 0.042 1909 Dihedral : 5.409 24.596 1473 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.43 % Allowed : 8.95 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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 (0.23), residues: 1320 helix: 0.31 (0.20), residues: 655 sheet: -0.63 (0.44), residues: 110 loop : -0.13 (0.28), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1265 HIS 0.006 0.001 HIS E 135 PHE 0.024 0.002 PHE D 744 TYR 0.023 0.002 TYR D 552 ARG 0.004 0.001 ARG A1529 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1305 PHE cc_start: 0.8169 (m-80) cc_final: 0.7661 (m-80) REVERT: A 1341 TYR cc_start: 0.8039 (t80) cc_final: 0.7796 (t80) REVERT: A 1453 PHE cc_start: 0.7546 (t80) cc_final: 0.6988 (t80) REVERT: A 1528 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7442 (m-30) REVERT: A 1530 MET cc_start: 0.6122 (mmm) cc_final: 0.5564 (mmm) REVERT: A 1545 LYS cc_start: 0.7853 (tttt) cc_final: 0.7510 (mptt) REVERT: A 1560 SER cc_start: 0.7167 (t) cc_final: 0.6800 (m) REVERT: A 1597 MET cc_start: 0.6298 (pmm) cc_final: 0.5888 (mpp) REVERT: A 1729 LEU cc_start: 0.9084 (mp) cc_final: 0.8750 (mt) REVERT: A 1806 MET cc_start: 0.7801 (mmm) cc_final: 0.6803 (mmm) REVERT: A 2054 LYS cc_start: 0.8636 (ttpt) cc_final: 0.8423 (ttmt) REVERT: A 2080 MET cc_start: 0.7059 (ttt) cc_final: 0.6708 (ttt) REVERT: D 472 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.7831 (mmm) REVERT: D 565 LYS cc_start: 0.9234 (pttt) cc_final: 0.8951 (ptpp) REVERT: D 568 MET cc_start: 0.9304 (mtp) cc_final: 0.8965 (mtt) REVERT: D 570 ARG cc_start: 0.8533 (mmm160) cc_final: 0.8087 (mmm160) REVERT: D 736 CYS cc_start: 0.8337 (t) cc_final: 0.7937 (m) REVERT: D 795 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8056 (mp10) REVERT: E 23 ARG cc_start: 0.7009 (mmt180) cc_final: 0.6806 (mmp80) REVERT: F 34 ASP cc_start: 0.7625 (t0) cc_final: 0.7250 (t0) REVERT: F 105 MET cc_start: 0.8759 (mmm) cc_final: 0.8116 (mmm) REVERT: F 106 THR cc_start: 0.8970 (m) cc_final: 0.8459 (p) outliers start: 29 outliers final: 16 residues processed: 174 average time/residue: 0.2665 time to fit residues: 64.3479 Evaluate side-chains 162 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1314 HIS Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1499 MET Chi-restraints excluded: chain A residue 1528 ASP Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1710 THR Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1744 GLU Chi-restraints excluded: chain A residue 1990 VAL Chi-restraints excluded: chain D residue 472 MET Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 795 GLN Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 104 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 121 optimal weight: 0.0050 chunk 128 optimal weight: 6.9990 chunk 63 optimal weight: 50.0000 chunk 115 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1550 ASN A1995 ASN A2024 HIS ** A2030 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 707 ASN D 739 ASN ** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 11020 Z= 0.411 Angle : 0.741 9.533 14902 Z= 0.378 Chirality : 0.045 0.284 1670 Planarity : 0.005 0.051 1909 Dihedral : 5.487 29.392 1473 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.68 % Allowed : 12.55 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.23), residues: 1320 helix: 0.20 (0.20), residues: 658 sheet: -0.52 (0.43), residues: 122 loop : -0.18 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A1265 HIS 0.007 0.001 HIS E 135 PHE 0.044 0.003 PHE D 744 TYR 0.021 0.002 TYR A1507 ARG 0.007 0.001 ARG A1509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1267 MET cc_start: 0.7933 (tpp) cc_final: 0.7663 (ttt) REVERT: A 1305 PHE cc_start: 0.8093 (m-80) cc_final: 0.7888 (m-80) REVERT: A 1341 TYR cc_start: 0.8100 (t80) cc_final: 0.7861 (t80) REVERT: A 1453 PHE cc_start: 0.7538 (t80) cc_final: 0.6965 (t80) REVERT: A 1469 MET cc_start: 0.8867 (tmm) cc_final: 0.8666 (tmm) REVERT: A 1528 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7299 (m-30) REVERT: A 1560 SER cc_start: 0.7546 (t) cc_final: 0.7079 (m) REVERT: A 1597 MET cc_start: 0.6480 (pmm) cc_final: 0.6149 (mpp) REVERT: A 1806 MET cc_start: 0.7743 (mmm) cc_final: 0.7030 (mmm) REVERT: A 1995 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8563 (p0) REVERT: D 472 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.7810 (mmm) REVERT: D 565 LYS cc_start: 0.9291 (pttt) cc_final: 0.9051 (ptpp) REVERT: D 568 MET cc_start: 0.9380 (mtp) cc_final: 0.9054 (mtt) REVERT: D 570 ARG cc_start: 0.8543 (mmm160) cc_final: 0.8091 (mmm160) REVERT: D 736 CYS cc_start: 0.8517 (t) cc_final: 0.8155 (m) REVERT: D 795 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8095 (mp10) REVERT: E 25 VAL cc_start: 0.9408 (t) cc_final: 0.9187 (m) REVERT: F 19 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: F 34 ASP cc_start: 0.7609 (t0) cc_final: 0.7270 (t0) REVERT: F 68 ASP cc_start: 0.8462 (m-30) cc_final: 0.8230 (m-30) REVERT: F 105 MET cc_start: 0.8830 (mmm) cc_final: 0.8317 (mmm) REVERT: F 106 THR cc_start: 0.8990 (m) cc_final: 0.8738 (m) outliers start: 32 outliers final: 14 residues processed: 168 average time/residue: 0.2917 time to fit residues: 68.7109 Evaluate side-chains 157 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1314 HIS Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1499 MET Chi-restraints excluded: chain A residue 1528 ASP Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1727 LEU Chi-restraints excluded: chain A residue 1995 ASN Chi-restraints excluded: chain A residue 2003 MET Chi-restraints excluded: chain D residue 472 MET Chi-restraints excluded: chain D residue 489 HIS Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 795 GLN Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 104 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1502 GLN A1995 ASN A2030 GLN D 707 ASN ** D 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 822 HIS ** D 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11020 Z= 0.208 Angle : 0.642 12.274 14902 Z= 0.325 Chirality : 0.042 0.274 1670 Planarity : 0.004 0.041 1909 Dihedral : 5.108 24.721 1473 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.26 % Allowed : 13.89 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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 (0.23), residues: 1320 helix: 0.39 (0.20), residues: 662 sheet: -0.46 (0.43), residues: 122 loop : -0.09 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A1265 HIS 0.008 0.001 HIS E 135 PHE 0.020 0.002 PHE D 744 TYR 0.013 0.001 TYR E 167 ARG 0.007 0.000 ARG A1509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1267 MET cc_start: 0.7885 (tpp) cc_final: 0.7611 (ttt) REVERT: A 1341 TYR cc_start: 0.8094 (t80) cc_final: 0.7865 (t80) REVERT: A 1453 PHE cc_start: 0.7503 (t80) cc_final: 0.6893 (t80) REVERT: A 1528 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7315 (m-30) REVERT: A 1530 MET cc_start: 0.6080 (mmm) cc_final: 0.5739 (mmm) REVERT: A 1560 SER cc_start: 0.7216 (t) cc_final: 0.6863 (m) REVERT: A 1597 MET cc_start: 0.6364 (pmm) cc_final: 0.6015 (mpp) REVERT: D 472 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.7791 (mmm) REVERT: D 565 LYS cc_start: 0.9281 (pttt) cc_final: 0.9031 (ptpp) REVERT: D 568 MET cc_start: 0.9338 (mtp) cc_final: 0.9017 (mtt) REVERT: D 570 ARG cc_start: 0.8367 (mmm160) cc_final: 0.8067 (mmp-170) REVERT: D 736 CYS cc_start: 0.8256 (t) cc_final: 0.7936 (m) REVERT: D 795 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8063 (mp10) REVERT: E 176 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7536 (mt) REVERT: F 19 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: F 34 ASP cc_start: 0.7646 (t0) cc_final: 0.7153 (t0) REVERT: F 56 GLN cc_start: 0.4074 (mt0) cc_final: 0.3633 (mm110) REVERT: F 68 ASP cc_start: 0.8450 (m-30) cc_final: 0.8204 (m-30) REVERT: F 96 LYS cc_start: 0.8630 (tppt) cc_final: 0.8381 (tptp) REVERT: F 106 THR cc_start: 0.8939 (m) cc_final: 0.8464 (p) outliers start: 27 outliers final: 14 residues processed: 162 average time/residue: 0.2532 time to fit residues: 57.4827 Evaluate side-chains 156 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1293 THR Chi-restraints excluded: chain A residue 1314 HIS Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1528 ASP Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1744 GLU Chi-restraints excluded: chain D residue 472 MET Chi-restraints excluded: chain D residue 489 HIS Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 795 GLN Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 82 HIS Chi-restraints excluded: chain F residue 104 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 67 optimal weight: 40.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1550 ASN ** A1995 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11020 Z= 0.274 Angle : 0.682 13.397 14902 Z= 0.342 Chirality : 0.042 0.245 1670 Planarity : 0.004 0.037 1909 Dihedral : 5.124 26.239 1473 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.51 % Allowed : 14.64 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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 (0.23), residues: 1320 helix: 0.40 (0.20), residues: 661 sheet: -0.58 (0.43), residues: 122 loop : -0.21 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1265 HIS 0.007 0.001 HIS E 135 PHE 0.030 0.002 PHE D 744 TYR 0.026 0.002 TYR D 756 ARG 0.004 0.000 ARG A1687 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1267 MET cc_start: 0.7945 (tpp) cc_final: 0.7626 (ttt) REVERT: A 1453 PHE cc_start: 0.7501 (t80) cc_final: 0.6930 (t80) REVERT: A 1528 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7308 (m-30) REVERT: A 1530 MET cc_start: 0.6196 (mmm) cc_final: 0.5578 (mmm) REVERT: A 1560 SER cc_start: 0.7396 (t) cc_final: 0.7057 (m) REVERT: A 1597 MET cc_start: 0.6466 (pmm) cc_final: 0.6135 (mpp) REVERT: D 472 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.7757 (mmm) REVERT: D 565 LYS cc_start: 0.9309 (pttt) cc_final: 0.9092 (ptpp) REVERT: D 568 MET cc_start: 0.9362 (mtp) cc_final: 0.9051 (mtt) REVERT: D 570 ARG cc_start: 0.8336 (mmm160) cc_final: 0.8103 (mmp-170) REVERT: D 736 CYS cc_start: 0.8437 (t) cc_final: 0.8141 (m) REVERT: D 795 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8043 (mp10) REVERT: E 176 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7630 (mt) REVERT: F 19 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: F 34 ASP cc_start: 0.7685 (t0) cc_final: 0.7153 (t0) REVERT: F 68 ASP cc_start: 0.8510 (m-30) cc_final: 0.8231 (m-30) REVERT: F 96 LYS cc_start: 0.8597 (tppt) cc_final: 0.8341 (tptp) outliers start: 30 outliers final: 18 residues processed: 163 average time/residue: 0.2619 time to fit residues: 60.1006 Evaluate side-chains 160 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1293 THR Chi-restraints excluded: chain A residue 1314 HIS Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1455 LEU Chi-restraints excluded: chain A residue 1528 ASP Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1744 GLU Chi-restraints excluded: chain D residue 472 MET Chi-restraints excluded: chain D residue 489 HIS Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 795 GLN Chi-restraints excluded: chain D residue 798 SER Chi-restraints excluded: chain D residue 844 VAL Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 82 HIS Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 104 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 108 optimal weight: 0.0970 chunk 71 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 78 optimal weight: 30.0000 chunk 59 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1550 ASN ** A1995 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 HIS ** D 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11020 Z= 0.202 Angle : 0.661 12.672 14902 Z= 0.327 Chirality : 0.041 0.202 1670 Planarity : 0.004 0.037 1909 Dihedral : 4.935 24.417 1473 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.09 % Allowed : 15.40 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1320 helix: 0.59 (0.20), residues: 661 sheet: -0.54 (0.43), residues: 122 loop : -0.18 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1265 HIS 0.009 0.001 HIS E 135 PHE 0.019 0.002 PHE D 744 TYR 0.021 0.001 TYR A1447 ARG 0.007 0.000 ARG A1509 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1267 MET cc_start: 0.7978 (tpp) cc_final: 0.7717 (ttt) REVERT: A 1268 GLN cc_start: 0.9054 (mp10) cc_final: 0.8799 (pm20) REVERT: A 1453 PHE cc_start: 0.7382 (t80) cc_final: 0.6776 (t80) REVERT: A 1528 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7357 (m-30) REVERT: A 1560 SER cc_start: 0.7224 (t) cc_final: 0.6869 (m) REVERT: A 1597 MET cc_start: 0.6416 (pmm) cc_final: 0.6136 (mpp) REVERT: D 472 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.7756 (mmm) REVERT: D 568 MET cc_start: 0.9300 (mtp) cc_final: 0.9002 (mtt) REVERT: D 570 ARG cc_start: 0.8266 (mmm160) cc_final: 0.8061 (mmp-170) REVERT: D 736 CYS cc_start: 0.8375 (t) cc_final: 0.8020 (m) REVERT: D 795 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8024 (mp10) REVERT: E 176 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7621 (mt) REVERT: E 177 ASP cc_start: 0.7756 (p0) cc_final: 0.7525 (p0) REVERT: F 19 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: F 34 ASP cc_start: 0.7646 (t0) cc_final: 0.7091 (t0) REVERT: F 68 ASP cc_start: 0.8469 (m-30) cc_final: 0.8173 (m-30) outliers start: 25 outliers final: 13 residues processed: 159 average time/residue: 0.2522 time to fit residues: 57.1015 Evaluate side-chains 155 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1314 HIS Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1374 LEU Chi-restraints excluded: chain A residue 1528 ASP Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1710 THR Chi-restraints excluded: chain D residue 472 MET Chi-restraints excluded: chain D residue 489 HIS Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 795 GLN Chi-restraints excluded: chain D residue 844 VAL Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 99 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 8.9990 chunk 51 optimal weight: 0.2980 chunk 76 optimal weight: 20.0000 chunk 38 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.0000 chunk 81 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 63 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1281 ASN ** A1478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1995 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2104 ASN ** D 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11020 Z= 0.198 Angle : 0.671 13.431 14902 Z= 0.328 Chirality : 0.041 0.235 1670 Planarity : 0.004 0.035 1909 Dihedral : 4.832 24.313 1473 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.51 % Allowed : 16.23 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.25 (0.23), residues: 1320 helix: 0.71 (0.20), residues: 657 sheet: -0.58 (0.44), residues: 123 loop : -0.18 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D 625 HIS 0.008 0.001 HIS E 135 PHE 0.020 0.002 PHE D 744 TYR 0.029 0.001 TYR D 756 ARG 0.007 0.000 ARG A1509 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1453 PHE cc_start: 0.7393 (t80) cc_final: 0.6775 (t80) REVERT: A 1530 MET cc_start: 0.6029 (mmm) cc_final: 0.5703 (mmm) REVERT: A 1545 LYS cc_start: 0.7734 (tttt) cc_final: 0.7299 (mptt) REVERT: A 1597 MET cc_start: 0.6379 (pmm) cc_final: 0.5836 (mpp) REVERT: D 472 MET cc_start: 0.8529 (ttt) cc_final: 0.7779 (mmm) REVERT: D 568 MET cc_start: 0.9286 (mtp) cc_final: 0.9006 (mtt) REVERT: D 736 CYS cc_start: 0.8483 (t) cc_final: 0.8099 (m) REVERT: D 795 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8017 (mp10) REVERT: E 176 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7649 (mt) REVERT: E 177 ASP cc_start: 0.7731 (p0) cc_final: 0.7485 (p0) REVERT: F 34 ASP cc_start: 0.7578 (t0) cc_final: 0.7041 (t0) REVERT: F 68 ASP cc_start: 0.8479 (m-30) cc_final: 0.8194 (m-30) outliers start: 18 outliers final: 12 residues processed: 149 average time/residue: 0.2628 time to fit residues: 54.8026 Evaluate side-chains 147 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1710 THR Chi-restraints excluded: chain D residue 489 HIS Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 795 GLN Chi-restraints excluded: chain D residue 844 VAL Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 99 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 93 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 30.0000 chunk 126 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1995 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11020 Z= 0.206 Angle : 0.694 12.799 14902 Z= 0.335 Chirality : 0.042 0.360 1670 Planarity : 0.004 0.036 1909 Dihedral : 4.802 24.349 1473 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.59 % Allowed : 16.32 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.23), residues: 1320 helix: 0.72 (0.20), residues: 658 sheet: -0.83 (0.42), residues: 131 loop : -0.19 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 625 HIS 0.007 0.001 HIS E 135 PHE 0.020 0.002 PHE D 744 TYR 0.044 0.001 TYR D 756 ARG 0.008 0.000 ARG A1509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1267 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7735 (ttt) REVERT: A 1453 PHE cc_start: 0.7420 (t80) cc_final: 0.6796 (t80) REVERT: A 1545 LYS cc_start: 0.7729 (tttt) cc_final: 0.7437 (mptt) REVERT: A 1597 MET cc_start: 0.6419 (pmm) cc_final: 0.5875 (mpp) REVERT: D 472 MET cc_start: 0.8495 (ttt) cc_final: 0.7759 (mmm) REVERT: D 568 MET cc_start: 0.9222 (mtp) cc_final: 0.8889 (mtt) REVERT: D 736 CYS cc_start: 0.8388 (t) cc_final: 0.8012 (m) REVERT: D 775 LEU cc_start: 0.8212 (tp) cc_final: 0.7689 (tp) REVERT: D 795 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8032 (mp10) REVERT: D 844 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8360 (p) REVERT: E 23 ARG cc_start: 0.7287 (mmp80) cc_final: 0.7061 (mmp80) REVERT: E 176 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7662 (mt) REVERT: E 177 ASP cc_start: 0.7796 (p0) cc_final: 0.7536 (p0) REVERT: F 34 ASP cc_start: 0.7662 (t0) cc_final: 0.7146 (t0) REVERT: F 49 ASP cc_start: 0.6566 (p0) cc_final: 0.6349 (p0) REVERT: F 68 ASP cc_start: 0.8473 (m-30) cc_final: 0.8172 (m-30) outliers start: 19 outliers final: 12 residues processed: 149 average time/residue: 0.2535 time to fit residues: 54.1163 Evaluate side-chains 149 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1314 HIS Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1710 THR Chi-restraints excluded: chain D residue 489 HIS Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 795 GLN Chi-restraints excluded: chain D residue 844 VAL Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 99 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 121 optimal weight: 0.0470 chunk 105 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 83 optimal weight: 0.2980 chunk 112 optimal weight: 0.5980 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1995 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 779 HIS ** D 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11020 Z= 0.197 Angle : 0.723 16.055 14902 Z= 0.348 Chirality : 0.043 0.335 1670 Planarity : 0.004 0.035 1909 Dihedral : 4.762 26.573 1473 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.59 % Allowed : 16.74 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.23), residues: 1320 helix: 0.74 (0.20), residues: 658 sheet: -0.79 (0.42), residues: 131 loop : -0.25 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP D 625 HIS 0.007 0.001 HIS E 135 PHE 0.023 0.002 PHE A1496 TYR 0.049 0.002 TYR D 756 ARG 0.003 0.000 ARG A2056 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2640 Ramachandran restraints generated. 1320 Oldfield, 0 Emsley, 1320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1267 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7802 (ttt) REVERT: A 1453 PHE cc_start: 0.7413 (t80) cc_final: 0.6793 (t80) REVERT: A 1545 LYS cc_start: 0.7730 (tttt) cc_final: 0.7425 (mptt) REVERT: A 1597 MET cc_start: 0.6419 (pmm) cc_final: 0.5967 (mpp) REVERT: A 1780 PHE cc_start: 0.7709 (p90) cc_final: 0.7132 (t80) REVERT: D 472 MET cc_start: 0.8534 (ttt) cc_final: 0.7814 (mmm) REVERT: D 495 SER cc_start: 0.9124 (m) cc_final: 0.8847 (p) REVERT: D 570 ARG cc_start: 0.8521 (ptt180) cc_final: 0.8292 (ptp-170) REVERT: D 736 CYS cc_start: 0.8625 (t) cc_final: 0.8105 (m) REVERT: D 795 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: D 844 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8328 (p) REVERT: E 176 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7627 (mt) REVERT: E 177 ASP cc_start: 0.7769 (p0) cc_final: 0.7500 (p0) REVERT: F 34 ASP cc_start: 0.7675 (t0) cc_final: 0.7166 (t0) REVERT: F 68 ASP cc_start: 0.8458 (m-30) cc_final: 0.8227 (m-30) outliers start: 19 outliers final: 12 residues processed: 151 average time/residue: 0.2363 time to fit residues: 51.3181 Evaluate side-chains 149 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1314 HIS Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1710 THR Chi-restraints excluded: chain D residue 489 HIS Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 620 LEU Chi-restraints excluded: chain D residue 795 GLN Chi-restraints excluded: chain D residue 844 VAL Chi-restraints excluded: chain D residue 853 LEU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 99 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.0870 chunk 97 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1995 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 741 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 HIS ** 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 = 0.4440 r_free = 0.4440 target = 0.174201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.129862 restraints weight = 20786.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.130404 restraints weight = 13312.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.129623 restraints weight = 12059.255| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11020 Z= 0.203 Angle : 0.738 13.824 14902 Z= 0.359 Chirality : 0.044 0.413 1670 Planarity : 0.004 0.040 1909 Dihedral : 4.745 25.788 1473 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.34 % Allowed : 17.32 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.14 (0.23), residues: 1320 helix: 0.70 (0.20), residues: 658 sheet: -0.78 (0.42), residues: 131 loop : -0.29 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP D 625 HIS 0.006 0.001 HIS E 135 PHE 0.019 0.002 PHE D 744 TYR 0.059 0.002 TYR A1501 ARG 0.003 0.000 ARG A2056 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2436.25 seconds wall clock time: 45 minutes 35.69 seconds (2735.69 seconds total)