Starting phenix.real_space_refine on Wed Aug 5 17:21:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hvy_52445/08_2026/9hvy_52445.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hvy_52445/08_2026/9hvy_52445.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 { model { file = "/net/cci-nas-00/data/ceres_data/9hvy_52445/08_2026/9hvy_52445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hvy_52445/08_2026/9hvy_52445.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hvy_52445/08_2026/9hvy_52445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hvy_52445/08_2026/9hvy_52445.map" } resolution = 3.5 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= -0.017 sd= 0.319 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 1 6.06 5 S 49 5.16 5 C 6632 2.51 5 N 1835 2.21 5 O 1939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10456 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1396, 10455 Classifications: {'peptide': 1396} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'PCIS': 1, 'PTRANS': 65, 'TRANS': 1329} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 593 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ARG:plan': 6, 'TYR:plan': 10, 'GLU:plan': 6, 'GLN:plan1': 12, 'PHE:plan': 9, 'ASP:plan': 8, 'HIS:plan': 3, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 277 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5278 SG CYS A1146 31.627 76.971 93.185 1.00 30.00 S ATOM 5292 SG CYS A1148 34.914 75.049 93.667 1.00 30.00 S ATOM 5312 SG CYS A1151 31.646 73.765 95.234 1.00 30.00 S Time building chain proxies: 2.51, per 1000 atoms: 0.24 Number of scatterers: 10456 At special positions: 0 Unit cell: (85.8792, 87.831, 170.783, 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 1 29.99 S 49 16.00 O 1939 8.00 N 1835 7.00 C 6632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 484 " - pdb=" SG CYS A 506 " distance=2.05 Simple disulfide: pdb=" SG CYS A 637 " - pdb=" SG CYS A 687 " distance=2.03 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: 0.89 Conformation dependent library (CDL) restraints added in 512.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2201 " pdb="ZN ZN A2201 " - pdb=" ND1 HIS A1142 " pdb="ZN ZN A2201 " - pdb=" SG CYS A1146 " pdb="ZN ZN A2201 " - pdb=" SG CYS A1151 " pdb="ZN ZN A2201 " - pdb=" SG CYS A1148 " Number of angles added : 3 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2640 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 2 sheets defined 74.1% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 331 through 352 Processing helix chain 'A' and resid 356 through 380 Processing helix chain 'A' and resid 389 through 415 Processing helix chain 'A' and resid 419 through 442 Processing helix chain 'A' and resid 451 through 470 Processing helix chain 'A' and resid 473 through 489 Proline residue: A 482 - end of helix Processing helix chain 'A' and resid 499 through 518 removed outlier: 3.622A pdb=" N PHE A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 534 Processing helix chain 'A' and resid 538 through 560 removed outlier: 4.424A pdb=" N GLU A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 561 through 567 removed outlier: 3.769A pdb=" N GLN A 565 " --> pdb=" O ASP A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 574 removed outlier: 3.768A pdb=" N SER A 572 " --> pdb=" O THR A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 595 Processing helix chain 'A' and resid 599 through 614 removed outlier: 3.683A pdb=" N ARG A 603 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 639 removed outlier: 4.266A pdb=" N TYR A 638 " --> pdb=" O GLN A 634 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS A 639 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 645 removed outlier: 3.529A pdb=" N THR A 645 " --> pdb=" O THR A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 663 Processing helix chain 'A' and resid 669 through 703 removed outlier: 4.714A pdb=" N ASP A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA A 678 " --> pdb=" O LEU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 Processing helix chain 'A' and resid 728 through 734 Processing helix chain 'A' and resid 735 through 737 No H-bonds generated for 'chain 'A' and resid 735 through 737' Processing helix chain 'A' and resid 738 through 760 removed outlier: 4.112A pdb=" N ALA A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 747 " --> pdb=" O GLN A 743 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS A 760 " --> pdb=" O GLU A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 removed outlier: 3.630A pdb=" N THR A 772 " --> pdb=" O CYS A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 807 removed outlier: 3.607A pdb=" N ALA A 792 " --> pdb=" O LYS A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 827 Processing helix chain 'A' and resid 828 through 844 removed outlier: 3.989A pdb=" N ALA A 832 " --> pdb=" O CYS A 828 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU A 834 " --> pdb=" O SER A 830 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS A 835 " --> pdb=" O TYR A 831 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS A 844 " --> pdb=" O ALA A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 871 removed outlier: 3.621A pdb=" N LEU A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 886 Processing helix chain 'A' and resid 894 through 912 removed outlier: 3.509A pdb=" N LEU A 899 " --> pdb=" O LYS A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 929 Processing helix chain 'A' and resid 934 through 954 Processing helix chain 'A' and resid 955 through 959 removed outlier: 4.053A pdb=" N ILE A 958 " --> pdb=" O GLY A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 1002 Processing helix chain 'A' and resid 1003 through 1022 Processing helix chain 'A' and resid 1023 through 1041 Processing helix chain 'A' and resid 1043 through 1062 Processing helix chain 'A' and resid 1138 through 1142 Processing helix chain 'A' and resid 1148 through 1153 Processing helix chain 'A' and resid 1153 through 1175 Processing helix chain 'A' and resid 1179 through 1207 Proline residue: A1192 - end of helix Processing helix chain 'A' and resid 1219 through 1237 removed outlier: 3.679A pdb=" N ASN A1236 " --> pdb=" O LEU A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1257 removed outlier: 3.569A pdb=" N GLN A1248 " --> pdb=" O GLN A1244 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG A1257 " --> pdb=" O PHE A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1278 Processing helix chain 'A' and resid 1288 through 1292 Processing helix chain 'A' and resid 1573 through 1586 Processing helix chain 'A' and resid 1593 through 1609 removed outlier: 3.583A pdb=" N ALA A1598 " --> pdb=" O SER A1594 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A1599 " --> pdb=" O GLY A1595 " (cutoff:3.500A) Processing helix chain 'A' and resid 1612 through 1622 Processing helix chain 'A' and resid 1625 through 1644 removed outlier: 3.659A pdb=" N ARG A1629 " --> pdb=" O SER A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1678 Processing helix chain 'A' and resid 1688 through 1701 removed outlier: 3.804A pdb=" N LEU A1701 " --> pdb=" O GLU A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1749 through 1769 removed outlier: 3.834A pdb=" N SER A1769 " --> pdb=" O LYS A1765 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1797 removed outlier: 3.570A pdb=" N GLU A1795 " --> pdb=" O ILE A1791 " (cutoff:3.500A) Processing helix chain 'A' and resid 1799 through 1801 No H-bonds generated for 'chain 'A' and resid 1799 through 1801' Processing helix chain 'A' and resid 1802 through 1807 removed outlier: 4.275A pdb=" N LEU A1806 " --> pdb=" O TRP A1802 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1828 removed outlier: 3.565A pdb=" N ARG A1821 " --> pdb=" O GLN A1817 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A1824 " --> pdb=" O SER A1820 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP A1828 " --> pdb=" O GLU A1824 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1845 removed outlier: 3.723A pdb=" N LEU A1839 " --> pdb=" O ASP A1835 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY A1845 " --> pdb=" O ILE A1841 " (cutoff:3.500A) Processing helix chain 'A' and resid 1850 through 1862 Processing helix chain 'A' and resid 1865 through 1881 Processing helix chain 'A' and resid 1903 through 1911 removed outlier: 3.656A pdb=" N SER A1906 " --> pdb=" O PRO A1903 " (cutoff:3.500A) Proline residue: A1908 - end of helix removed outlier: 3.626A pdb=" N GLN A1911 " --> pdb=" O PRO A1908 " (cutoff:3.500A) Processing helix chain 'A' and resid 1921 through 1933 removed outlier: 3.931A pdb=" N LEU A1925 " --> pdb=" O PHE A1921 " (cutoff:3.500A) Processing helix chain 'A' and resid 1936 through 1941 Processing helix chain 'A' and resid 1959 through 1965 Processing helix chain 'A' and resid 1966 through 1971 Processing helix chain 'A' and resid 1984 through 1994 Processing helix chain 'A' and resid 2011 through 2018 Processing helix chain 'A' and resid 2044 through 2052 removed outlier: 3.673A pdb=" N LYS A2048 " --> pdb=" O GLY A2044 " (cutoff:3.500A) Processing helix chain 'A' and resid 2067 through 2084 removed outlier: 4.400A pdb=" N GLY A2084 " --> pdb=" O TRP A2080 " (cutoff:3.500A) Processing helix chain 'A' and resid 2088 through 2097 removed outlier: 3.803A pdb=" N TYR A2092 " --> pdb=" O PRO A2088 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1737 through 1742 removed outlier: 3.759A pdb=" N VAL A1737 " --> pdb=" O ARG A1729 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A1729 " --> pdb=" O VAL A1737 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1975 through 1979 removed outlier: 3.565A pdb=" N TYR A1950 " --> pdb=" O ARG A1976 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR A1998 " --> pdb=" O LEU A2025 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A2024 " --> pdb=" O LEU A2058 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ASN A2060 " --> pdb=" O ALA A2024 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N LEU A2026 " --> pdb=" O ASN A2060 " (cutoff:3.500A) 745 hydrogen bonds defined for protein. 2214 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: 2.17 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3502 1.35 - 1.47: 2265 1.47 - 1.59: 4822 1.59 - 1.72: 0 1.72 - 1.84: 60 Bond restraints: 10649 Sorted by residual: bond pdb=" N ILE A 528 " pdb=" CA ILE A 528 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.43e+00 bond pdb=" N VAL A 498 " pdb=" CA VAL A 498 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.23e-02 6.61e+03 7.59e+00 bond pdb=" N VAL A 527 " pdb=" CA VAL A 527 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.26e-02 6.30e+03 7.31e+00 bond pdb=" N ILE A 958 " pdb=" CA ILE A 958 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.26e-02 6.30e+03 7.23e+00 bond pdb=" N LEU A1202 " pdb=" CA LEU A1202 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.56e+00 ... (remaining 10644 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 14176 2.19 - 4.38: 277 4.38 - 6.57: 29 6.57 - 8.76: 13 8.76 - 10.95: 2 Bond angle restraints: 14497 Sorted by residual: angle pdb=" N PRO A 331 " pdb=" CA PRO A 331 " pdb=" CB PRO A 331 " ideal model delta sigma weight residual 103.00 110.42 -7.42 1.10e+00 8.26e-01 4.54e+01 angle pdb=" N PRO A 332 " pdb=" CA PRO A 332 " pdb=" CB PRO A 332 " ideal model delta sigma weight residual 103.33 110.14 -6.81 1.10e+00 8.26e-01 3.84e+01 angle pdb=" CB ARG A 558 " pdb=" CG ARG A 558 " pdb=" CD ARG A 558 " ideal model delta sigma weight residual 111.30 120.17 -8.87 2.30e+00 1.89e-01 1.49e+01 angle pdb=" CA GLU A 481 " pdb=" CB GLU A 481 " pdb=" CG GLU A 481 " ideal model delta sigma weight residual 114.10 121.62 -7.52 2.00e+00 2.50e-01 1.41e+01 angle pdb=" N LEU A1219 " pdb=" CA LEU A1219 " pdb=" C LEU A1219 " ideal model delta sigma weight residual 113.30 108.37 4.93 1.34e+00 5.57e-01 1.36e+01 ... (remaining 14492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 5880 17.85 - 35.71: 422 35.71 - 53.56: 107 53.56 - 71.41: 47 71.41 - 89.27: 9 Dihedral angle restraints: 6465 sinusoidal: 2408 harmonic: 4057 Sorted by residual: dihedral pdb=" CB CYS A 637 " pdb=" SG CYS A 637 " pdb=" SG CYS A 687 " pdb=" CB CYS A 687 " ideal model delta sinusoidal sigma weight residual -86.00 -165.06 79.06 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CA LEU A 673 " pdb=" C LEU A 673 " pdb=" N LEU A 674 " pdb=" CA LEU A 674 " ideal model delta harmonic sigma weight residual 180.00 162.11 17.89 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ASP A 675 " pdb=" C ASP A 675 " pdb=" N ASP A 676 " pdb=" CA ASP A 676 " ideal model delta harmonic sigma weight residual 180.00 162.46 17.54 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 6462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1390 0.046 - 0.092: 246 0.092 - 0.138: 61 0.138 - 0.183: 10 0.183 - 0.229: 6 Chirality restraints: 1713 Sorted by residual: chirality pdb=" CA PRO A 331 " pdb=" N PRO A 331 " pdb=" C PRO A 331 " pdb=" CB PRO A 331 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA PRO A 332 " pdb=" N PRO A 332 " pdb=" C PRO A 332 " pdb=" CB PRO A 332 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA TYR A 495 " pdb=" N TYR A 495 " pdb=" C TYR A 495 " pdb=" CB TYR A 495 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.81e-01 ... (remaining 1710 not shown) Planarity restraints: 1864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 675 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C ASP A 675 " -0.063 2.00e-02 2.50e+03 pdb=" O ASP A 675 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP A 676 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A1953 " 0.057 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO A1954 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A1954 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A1954 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1687 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO A1688 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A1688 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1688 " 0.023 5.00e-02 4.00e+02 ... (remaining 1861 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 88 2.64 - 3.20: 9750 3.20 - 3.77: 16518 3.77 - 4.33: 20620 4.33 - 4.90: 33988 Nonbonded interactions: 80964 Sorted by model distance: nonbonded pdb=" O ARG A1879 " pdb=" NH1 ARG A1879 " model vdw 2.073 3.120 nonbonded pdb=" N GLN A1852 " pdb=" OE1 GLN A1852 " model vdw 2.213 3.120 nonbonded pdb=" N GLU A 563 " pdb=" OE1 GLU A 563 " model vdw 2.234 3.120 nonbonded pdb=" ND2 ASN A1953 " pdb=" OE1 GLU A1962 " model vdw 2.235 3.120 nonbonded pdb=" NH1 ARG A1729 " pdb=" O LEU A1805 " model vdw 2.305 3.120 ... (remaining 80959 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.950 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.760 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 : 0.004 0.067 10655 Z= 0.253 Angle : 0.702 10.947 14504 Z= 0.418 Chirality : 0.040 0.229 1713 Planarity : 0.005 0.085 1864 Dihedral : 14.603 89.266 3819 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.37 % Allowed : 13.67 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 are not related in a simple way. whole: 1.95 (0.23), residues: 1380 helix: 2.29 (0.16), residues: 953 sheet: 1.33 (0.81), residues: 48 loop : -1.45 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 558 TYR 0.031 0.001 TYR A 973 PHE 0.018 0.002 PHE A 735 TRP 0.017 0.001 TRP A1776 HIS 0.012 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.25 (10649) covalent geometry : angle 0.70129 / 0.42 (14497) SS BOND : bond 0.01090 / 0.72 ( 2) SS BOND : angle 2.09896 / 1.50 ( 4) hydrogen bonds : bond 0.15696 / 12.00 ( 745) hydrogen bonds : angle 4.91365 / 3.70 ( 2214) metal coordination : bond 0.01258 / 0.81 ( 4) metal coordination : angle 0.80095 / 0.42 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 954 MET cc_start: 0.8273 (mtm) cc_final: 0.8031 (mtm) REVERT: A 1218 LEU cc_start: 0.7638 (tp) cc_final: 0.7377 (tp) outliers start: 4 outliers final: 1 residues processed: 132 average time/residue: 0.1560 time to fit residues: 26.7149 Evaluate side-chains 111 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 959 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 522 GLN A 535 GLN A 601 GLN A 605 ASN A 933 GLN A1048 GLN A1295 GLN A1599 HIS A1941 GLN A1964 GLN A2060 ASN A2098 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.057273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.047461 restraints weight = 38987.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.048731 restraints weight = 19954.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.049563 restraints weight = 12649.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.050118 restraints weight = 9240.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.050461 restraints weight = 7407.722| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10655 Z= 0.161 Angle : 0.601 8.956 14504 Z= 0.307 Chirality : 0.037 0.174 1713 Planarity : 0.005 0.054 1864 Dihedral : 4.093 41.849 1482 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.97 % Allowed : 13.11 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 are not related in a simple way. whole: 1.97 (0.23), residues: 1380 helix: 2.22 (0.16), residues: 970 sheet: 1.57 (0.78), residues: 48 loop : -1.35 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 508 TYR 0.017 0.001 TYR A2104 PHE 0.019 0.002 PHE A 728 TRP 0.015 0.001 TRP A1776 HIS 0.006 0.001 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (10649) covalent geometry : angle 0.59961 / 0.31 (14497) SS BOND : bond 0.00504 / 0.33 ( 2) SS BOND : angle 2.14845 / 1.53 ( 4) hydrogen bonds : bond 0.06167 / 4.73 ( 745) hydrogen bonds : angle 4.24142 / 3.21 ( 2214) metal coordination : bond 0.02154 / 1.41 ( 4) metal coordination : angle 2.11025 / 1.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 526 MET cc_start: 0.8134 (mtm) cc_final: 0.7493 (mtp) REVERT: A 1199 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8292 (m) outliers start: 21 outliers final: 8 residues processed: 132 average time/residue: 0.1391 time to fit residues: 24.4410 Evaluate side-chains 120 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1288 PHE Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 2046 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1208 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.056421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.046513 restraints weight = 39012.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.047794 restraints weight = 19973.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.048630 restraints weight = 12696.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.049174 restraints weight = 9259.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.049550 restraints weight = 7445.394| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10655 Z= 0.160 Angle : 0.582 8.102 14504 Z= 0.298 Chirality : 0.037 0.166 1713 Planarity : 0.005 0.046 1864 Dihedral : 4.114 40.803 1482 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.43 % Allowed : 12.73 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 are not related in a simple way. whole: 1.94 (0.23), residues: 1380 helix: 2.18 (0.16), residues: 984 sheet: 1.61 (0.76), residues: 48 loop : -1.47 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 702 TYR 0.015 0.001 TYR A2104 PHE 0.015 0.002 PHE A 728 TRP 0.015 0.001 TRP A1776 HIS 0.010 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (10649) covalent geometry : angle 0.57911 / 0.30 (14497) SS BOND : bond 0.00571 / 0.37 ( 2) SS BOND : angle 2.70257 / 1.79 ( 4) hydrogen bonds : bond 0.05761 / 4.42 ( 745) hydrogen bonds : angle 4.08641 / 3.09 ( 2214) metal coordination : bond 0.02599 / 1.71 ( 4) metal coordination : angle 2.35369 / 1.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 ARG cc_start: 0.7738 (ttt-90) cc_final: 0.7518 (ttt-90) REVERT: A 567 LYS cc_start: 0.8569 (ptpp) cc_final: 0.7832 (ptpp) REVERT: A 1842 MET cc_start: 0.8956 (mmm) cc_final: 0.8600 (mpp) outliers start: 26 outliers final: 18 residues processed: 130 average time/residue: 0.1382 time to fit residues: 24.0965 Evaluate side-chains 130 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1288 PHE Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1707 THR Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 2046 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 81 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.056536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.046705 restraints weight = 39118.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.047997 restraints weight = 19942.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.048833 restraints weight = 12602.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.049384 restraints weight = 9161.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.049732 restraints weight = 7342.789| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10655 Z= 0.144 Angle : 0.578 11.518 14504 Z= 0.294 Chirality : 0.036 0.135 1713 Planarity : 0.005 0.046 1864 Dihedral : 4.071 40.222 1482 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.15 % Allowed : 14.61 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 are not related in a simple way. whole: 2.08 (0.23), residues: 1380 helix: 2.27 (0.16), residues: 984 sheet: 1.66 (0.75), residues: 48 loop : -1.40 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A2017 TYR 0.012 0.001 TYR A2092 PHE 0.013 0.001 PHE A 728 TRP 0.016 0.001 TRP A1776 HIS 0.008 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (10649) covalent geometry : angle 0.57581 / 0.29 (14497) SS BOND : bond 0.00426 / 0.28 ( 2) SS BOND : angle 2.49683 / 1.67 ( 4) hydrogen bonds : bond 0.05295 / 4.06 ( 745) hydrogen bonds : angle 3.97624 / 3.01 ( 2214) metal coordination : bond 0.02286 / 1.51 ( 4) metal coordination : angle 2.32437 / 1.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1966 ARG cc_start: 0.7103 (ttm-80) cc_final: 0.6879 (ttm-80) outliers start: 23 outliers final: 18 residues processed: 127 average time/residue: 0.1363 time to fit residues: 23.1870 Evaluate side-chains 126 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1288 PHE Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1707 THR Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 2046 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 38 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 30 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 68.6298 > 50:) chunk 6 optimal weight: 10.0000 chunk 99 optimal weight: 0.0170 chunk 58 optimal weight: 1.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 541 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 = 0.3087 r_free = 0.3087 target = 0.056709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.046749 restraints weight = 39011.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.048031 restraints weight = 19764.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.048865 restraints weight = 12447.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.049410 restraints weight = 9063.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.049754 restraints weight = 7266.349| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10655 Z= 0.139 Angle : 0.578 11.500 14504 Z= 0.294 Chirality : 0.036 0.196 1713 Planarity : 0.005 0.049 1864 Dihedral : 4.042 40.178 1482 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.25 % Allowed : 15.54 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 are not related in a simple way. whole: 2.24 (0.23), residues: 1380 helix: 2.39 (0.16), residues: 980 sheet: 1.66 (0.76), residues: 48 loop : -1.26 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 505 TYR 0.011 0.001 TYR A2092 PHE 0.013 0.001 PHE A 728 TRP 0.015 0.001 TRP A1776 HIS 0.004 0.001 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (10649) covalent geometry : angle 0.57506 / 0.29 (14497) SS BOND : bond 0.00545 / 0.36 ( 2) SS BOND : angle 2.89272 / 1.80 ( 4) hydrogen bonds : bond 0.05052 / 3.87 ( 745) hydrogen bonds : angle 3.90856 / 2.96 ( 2214) metal coordination : bond 0.02160 / 1.42 ( 4) metal coordination : angle 2.19299 / 1.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 ARG cc_start: 0.7970 (ttt180) cc_final: 0.7729 (ttt180) REVERT: A 767 ARG cc_start: 0.8202 (ttm110) cc_final: 0.7807 (ttm110) outliers start: 24 outliers final: 22 residues processed: 128 average time/residue: 0.1426 time to fit residues: 24.3975 Evaluate side-chains 132 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1288 PHE Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1707 THR Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 1885 VAL Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 2046 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 15 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 107 optimal weight: 0.0010 chunk 72 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 112 optimal weight: 0.0170 chunk 36 optimal weight: 0.0970 overall best weight: 0.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 541 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 = 0.3115 r_free = 0.3115 target = 0.057776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.047977 restraints weight = 39586.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.049276 restraints weight = 20056.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.050131 restraints weight = 12634.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.050700 restraints weight = 9154.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.051049 restraints weight = 7285.750| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10655 Z= 0.120 Angle : 0.558 11.368 14504 Z= 0.285 Chirality : 0.035 0.191 1713 Planarity : 0.005 0.047 1864 Dihedral : 3.994 40.669 1482 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.78 % Allowed : 16.85 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 are not related in a simple way. whole: 2.48 (0.23), residues: 1380 helix: 2.56 (0.16), residues: 980 sheet: 1.79 (0.77), residues: 48 loop : -1.16 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 558 TYR 0.010 0.001 TYR A2092 PHE 0.011 0.001 PHE A 728 TRP 0.013 0.001 TRP A1776 HIS 0.004 0.001 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (10649) covalent geometry : angle 0.55677 / 0.28 (14497) SS BOND : bond 0.00253 / 0.16 ( 2) SS BOND : angle 2.19927 / 1.49 ( 4) hydrogen bonds : bond 0.04358 / 3.35 ( 745) hydrogen bonds : angle 3.74347 / 2.83 ( 2214) metal coordination : bond 0.01259 / 0.83 ( 4) metal coordination : angle 1.50193 / 0.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 ARG cc_start: 0.7902 (ttt180) cc_final: 0.7609 (tmt170) REVERT: A 767 ARG cc_start: 0.8158 (ttm110) cc_final: 0.7765 (ttm110) REVERT: A 1966 ARG cc_start: 0.7284 (ttm-80) cc_final: 0.6968 (ttm-80) outliers start: 19 outliers final: 12 residues processed: 132 average time/residue: 0.1525 time to fit residues: 26.5140 Evaluate side-chains 122 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1288 PHE Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1707 THR Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1873 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 1 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 62 optimal weight: 0.0040 chunk 113 optimal weight: 0.0770 chunk 107 optimal weight: 0.0010 chunk 12 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 overall best weight: 0.2556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.058340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.048488 restraints weight = 38931.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.049773 restraints weight = 19717.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.050606 restraints weight = 12462.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.051163 restraints weight = 9096.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.051533 restraints weight = 7292.725| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10655 Z= 0.123 Angle : 0.583 10.255 14504 Z= 0.296 Chirality : 0.035 0.185 1713 Planarity : 0.004 0.048 1864 Dihedral : 3.968 40.362 1482 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.87 % Allowed : 17.23 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 are not related in a simple way. whole: 2.56 (0.23), residues: 1380 helix: 2.61 (0.16), residues: 980 sheet: 1.83 (0.78), residues: 48 loop : -1.09 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A2017 TYR 0.010 0.001 TYR A 730 PHE 0.010 0.001 PHE A 728 TRP 0.011 0.001 TRP A1776 HIS 0.004 0.000 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (10649) covalent geometry : angle 0.58172 / 0.30 (14497) SS BOND : bond 0.00276 / 0.18 ( 2) SS BOND : angle 2.18434 / 1.38 ( 4) hydrogen bonds : bond 0.04104 / 3.16 ( 745) hydrogen bonds : angle 3.69567 / 2.80 ( 2214) metal coordination : bond 0.00980 / 0.64 ( 4) metal coordination : angle 1.18915 / 0.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 767 ARG cc_start: 0.8183 (ttm110) cc_final: 0.7794 (ttm110) REVERT: A 1966 ARG cc_start: 0.7216 (ttm-80) cc_final: 0.6905 (ttm-80) outliers start: 20 outliers final: 17 residues processed: 129 average time/residue: 0.1388 time to fit residues: 23.8700 Evaluate side-chains 127 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1288 PHE Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1707 THR Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 2046 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 12 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 chunk 57 optimal weight: 0.0670 chunk 107 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 104 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 93 optimal weight: 0.9980 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 504 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.058174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.048479 restraints weight = 38926.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.049767 restraints weight = 19810.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.050600 restraints weight = 12490.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.051176 restraints weight = 9057.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.051517 restraints weight = 7210.657| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10655 Z= 0.124 Angle : 0.590 12.068 14504 Z= 0.297 Chirality : 0.035 0.174 1713 Planarity : 0.004 0.049 1864 Dihedral : 3.929 39.409 1482 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.69 % Allowed : 17.88 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 are not related in a simple way. whole: 2.58 (0.23), residues: 1380 helix: 2.62 (0.16), residues: 983 sheet: 1.82 (0.78), residues: 48 loop : -1.12 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A2017 TYR 0.010 0.001 TYR A2092 PHE 0.010 0.001 PHE A 735 TRP 0.012 0.001 TRP A1776 HIS 0.005 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (10649) covalent geometry : angle 0.58803 / 0.30 (14497) SS BOND : bond 0.00344 / 0.22 ( 2) SS BOND : angle 2.42634 / 1.50 ( 4) hydrogen bonds : bond 0.04116 / 3.16 ( 745) hydrogen bonds : angle 3.66088 / 2.77 ( 2214) metal coordination : bond 0.01116 / 0.73 ( 4) metal coordination : angle 1.20160 / 0.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 HIS cc_start: 0.7824 (OUTLIER) cc_final: 0.6973 (m-70) REVERT: A 505 ARG cc_start: 0.7714 (ttt180) cc_final: 0.7471 (ttt180) REVERT: A 767 ARG cc_start: 0.8147 (ttm110) cc_final: 0.7752 (ttm110) REVERT: A 1966 ARG cc_start: 0.7258 (ttm-80) cc_final: 0.6866 (ttm-80) outliers start: 18 outliers final: 15 residues processed: 125 average time/residue: 0.1376 time to fit residues: 23.0001 Evaluate side-chains 122 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1288 PHE Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1707 THR Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 2046 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 110 optimal weight: 3.9990 chunk 94 optimal weight: 0.0970 chunk 66 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 504 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 = 0.3103 r_free = 0.3103 target = 0.057463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.047721 restraints weight = 39382.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.049000 restraints weight = 19987.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.049818 restraints weight = 12621.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.050376 restraints weight = 9227.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.050758 restraints weight = 7413.147| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10655 Z= 0.137 Angle : 0.607 11.744 14504 Z= 0.308 Chirality : 0.036 0.248 1713 Planarity : 0.005 0.050 1864 Dihedral : 3.986 38.431 1482 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.97 % Allowed : 17.79 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 are not related in a simple way. whole: 2.47 (0.23), residues: 1380 helix: 2.56 (0.16), residues: 975 sheet: 1.80 (0.77), residues: 48 loop : -1.12 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A2017 TYR 0.014 0.001 TYR A 495 PHE 0.010 0.001 PHE A1030 TRP 0.013 0.001 TRP A1776 HIS 0.014 0.001 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (10649) covalent geometry : angle 0.60634 / 0.31 (14497) SS BOND : bond 0.00370 / 0.24 ( 2) SS BOND : angle 2.06028 / 1.38 ( 4) hydrogen bonds : bond 0.04464 / 3.43 ( 745) hydrogen bonds : angle 3.69745 / 2.80 ( 2214) metal coordination : bond 0.01630 / 1.07 ( 4) metal coordination : angle 1.41852 / 0.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 ARG cc_start: 0.7752 (ttt180) cc_final: 0.7544 (ttt180) REVERT: A 702 ARG cc_start: 0.7770 (ttp80) cc_final: 0.7568 (ttp80) REVERT: A 767 ARG cc_start: 0.8153 (ttm110) cc_final: 0.7743 (ttm110) outliers start: 21 outliers final: 19 residues processed: 122 average time/residue: 0.1433 time to fit residues: 23.3422 Evaluate side-chains 123 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1288 PHE Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1707 THR Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1853 ASP Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 2018 LEU Chi-restraints excluded: chain A residue 2046 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 16 optimal weight: 9.9990 chunk 67 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 504 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 = 0.3072 r_free = 0.3072 target = 0.056232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.046359 restraints weight = 39210.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.047614 restraints weight = 19939.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.048440 restraints weight = 12676.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.048990 restraints weight = 9267.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.049357 restraints weight = 7467.068| |-----------------------------------------------------------------------------| r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10655 Z= 0.161 Angle : 0.647 11.608 14504 Z= 0.329 Chirality : 0.037 0.245 1713 Planarity : 0.005 0.055 1864 Dihedral : 4.087 37.123 1482 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.69 % Allowed : 18.16 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 are not related in a simple way. whole: 2.26 (0.23), residues: 1380 helix: 2.37 (0.16), residues: 989 sheet: 1.26 (0.75), residues: 54 loop : -1.22 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1836 TYR 0.013 0.001 TYR A2092 PHE 0.013 0.001 PHE A1030 TRP 0.015 0.001 TRP A1776 HIS 0.002 0.001 HIS A1955 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (10649) covalent geometry : angle 0.64531 / 0.33 (14497) SS BOND : bond 0.00398 / 0.26 ( 2) SS BOND : angle 2.64369 / 1.60 ( 4) hydrogen bonds : bond 0.05125 / 3.93 ( 745) hydrogen bonds : angle 3.80035 / 2.87 ( 2214) metal coordination : bond 0.02378 / 1.57 ( 4) metal coordination : angle 2.10910 / 1.36 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 ARG cc_start: 0.7819 (ttt180) cc_final: 0.7482 (tmt170) REVERT: A 542 MET cc_start: 0.8752 (tpp) cc_final: 0.8471 (tpp) REVERT: A 702 ARG cc_start: 0.7823 (ttp80) cc_final: 0.7605 (ttp80) REVERT: A 767 ARG cc_start: 0.8195 (ttm110) cc_final: 0.7783 (ttm110) outliers start: 18 outliers final: 17 residues processed: 120 average time/residue: 0.1488 time to fit residues: 23.7290 Evaluate side-chains 123 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1288 PHE Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1707 THR Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1853 ASP Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 2046 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 91 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 504 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 = 0.3071 r_free = 0.3071 target = 0.056169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.046378 restraints weight = 39297.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.047651 restraints weight = 19954.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.048484 restraints weight = 12563.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.049024 restraints weight = 9129.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.049386 restraints weight = 7359.594| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10655 Z= 0.152 Angle : 0.636 11.705 14504 Z= 0.324 Chirality : 0.037 0.231 1713 Planarity : 0.005 0.083 1864 Dihedral : 4.083 36.711 1482 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.69 % Allowed : 18.35 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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 are not related in a simple way. whole: 2.24 (0.23), residues: 1380 helix: 2.35 (0.16), residues: 989 sheet: 1.28 (0.75), residues: 54 loop : -1.21 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A2017 TYR 0.012 0.001 TYR A2092 PHE 0.012 0.001 PHE A1030 TRP 0.016 0.001 TRP A1776 HIS 0.003 0.001 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (10649) covalent geometry : angle 0.63422 / 0.32 (14497) SS BOND : bond 0.00372 / 0.24 ( 2) SS BOND : angle 2.69345 / 1.64 ( 4) hydrogen bonds : bond 0.04991 / 3.83 ( 745) hydrogen bonds : angle 3.78646 / 2.86 ( 2214) metal coordination : bond 0.02235 / 1.47 ( 4) metal coordination : angle 2.18263 / 1.36 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1732.01 seconds wall clock time: 30 minutes 45.70 seconds (1845.70 seconds total)