Starting phenix.real_space_refine on Wed Feb 4 11:52:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hm7_52288/02_2026/9hm7_52288.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hm7_52288/02_2026/9hm7_52288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hm7_52288/02_2026/9hm7_52288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hm7_52288/02_2026/9hm7_52288.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hm7_52288/02_2026/9hm7_52288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hm7_52288/02_2026/9hm7_52288.map" } resolution = 3.1 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= -0.020 sd= 0.329 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 47 5.16 5 C 6443 2.51 5 N 1777 2.21 5 O 1882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10150 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10149 Classifications: {'peptide': 1340} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PCIS': 2, 'PTRANS': 65, 'TRANS': 1272} Chain breaks: 7 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 4, 'TRP:plan': 1, 'GLU:plan': 9, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 150 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 4797 SG CYS A1146 34.889 8.449 74.096 1.00 30.00 S ATOM 4811 SG CYS A1148 39.092 9.823 75.957 1.00 30.00 S ATOM 4831 SG CYS A1151 37.125 12.439 73.893 1.00 30.00 S Time building chain proxies: 2.05, per 1000 atoms: 0.20 Number of scatterers: 10150 At special positions: 0 Unit cell: (84.9033, 87.831, 155.168, 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 47 16.00 O 1882 8.00 N 1777 7.00 C 6443 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 637 " - pdb=" SG CYS A 687 " distance=2.04 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: 0.75 Conformation dependent library (CDL) restraints added in 435.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2201 " pdb="ZN ZN A2201 " - pdb=" SG CYS A1148 " pdb="ZN ZN A2201 " - pdb=" SG CYS A1151 " pdb="ZN ZN A2201 " - pdb=" ND1 HIS A1142 " pdb="ZN ZN A2201 " - pdb=" SG CYS A1146 " Number of angles added : 3 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2538 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 2 sheets defined 71.6% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 422 through 442 Processing helix chain 'A' and resid 446 through 470 Processing helix chain 'A' and resid 472 through 491 Proline residue: A 482 - end of helix Processing helix chain 'A' and resid 501 through 517 Processing helix chain 'A' and resid 520 through 534 removed outlier: 4.093A pdb=" N LYS A 525 " --> pdb=" O ALA A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 560 removed outlier: 3.891A pdb=" N THR A 547 " --> pdb=" O ALA A 543 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 556 " --> pdb=" O VAL A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 567 removed outlier: 3.520A pdb=" N LYS A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 574 Processing helix chain 'A' and resid 577 through 595 removed outlier: 3.747A pdb=" N ALA A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 614 Processing helix chain 'A' and resid 618 through 639 removed outlier: 3.659A pdb=" N TRP A 623 " --> pdb=" O PRO A 619 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A 631 " --> pdb=" O THR A 627 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 638 " --> pdb=" O GLN A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 648 through 662 Processing helix chain 'A' and resid 669 through 674 removed outlier: 3.508A pdb=" N LEU A 674 " --> pdb=" O ARG A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 704 Processing helix chain 'A' and resid 710 through 715 removed outlier: 3.944A pdb=" N GLU A 713 " --> pdb=" O GLU A 710 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 714 " --> pdb=" O GLU A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 724 Processing helix chain 'A' and resid 738 through 760 removed outlier: 3.657A pdb=" N CYS A 746 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 747 " --> pdb=" O GLN A 743 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS A 760 " --> pdb=" O GLU A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 removed outlier: 3.589A pdb=" N THR A 772 " --> pdb=" O CYS A 768 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 778 " --> pdb=" O ALA A 774 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN A 784 " --> pdb=" O ALA A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 807 removed outlier: 3.533A pdb=" N GLU A 794 " --> pdb=" O MET A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 826 Processing helix chain 'A' and resid 828 through 844 removed outlier: 3.630A pdb=" N GLN A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 834 " --> pdb=" O SER A 830 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS A 835 " --> pdb=" O TYR A 831 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS A 844 " --> pdb=" O ALA A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 871 removed outlier: 3.563A pdb=" N LEU A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 886 removed outlier: 3.540A pdb=" N GLY A 877 " --> pdb=" O LYS A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 892 removed outlier: 3.835A pdb=" N GLN A 891 " --> pdb=" O PRO A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 913 Processing helix chain 'A' and resid 914 through 919 removed outlier: 6.252A pdb=" N ASN A 917 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 919 " --> pdb=" O SER A 916 " (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 974 through 1002 removed outlier: 3.566A pdb=" N VAL A 978 " --> pdb=" O GLY A 974 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TRP A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 984 " --> pdb=" O LYS A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1022 removed outlier: 3.501A pdb=" N ALA A1009 " --> pdb=" O SER A1005 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A1010 " --> pdb=" O GLU A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1041 removed outlier: 3.566A pdb=" N LEU A1029 " --> pdb=" O ARG A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1062 Processing helix chain 'A' and resid 1153 through 1174 Processing helix chain 'A' and resid 1179 through 1207 removed outlier: 3.603A pdb=" N VAL A1186 " --> pdb=" O ASP A1182 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A1187 " --> pdb=" O LEU A1183 " (cutoff:3.500A) Proline residue: A1192 - end of helix removed outlier: 3.717A pdb=" N ALA A1204 " --> pdb=" O GLN A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1237 removed outlier: 3.882A pdb=" N LEU A1235 " --> pdb=" O ALA A1231 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASN A1236 " --> pdb=" O LEU A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1256 removed outlier: 3.984A pdb=" N LYS A1245 " --> pdb=" O GLU A1241 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL A1246 " --> pdb=" O SER A1242 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A1247 " --> pdb=" O LEU A1243 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN A1248 " --> pdb=" O GLN A1244 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A1253 " --> pdb=" O SER A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1278 Processing helix chain 'A' and resid 1285 through 1292 removed outlier: 3.586A pdb=" N ALA A1289 " --> pdb=" O GLN A1286 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER A1290 " --> pdb=" O LEU A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1573 through 1589 removed outlier: 3.568A pdb=" N VAL A1583 " --> pdb=" O ASP A1579 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A1588 " --> pdb=" O ALA A1584 " (cutoff:3.500A) Processing helix chain 'A' and resid 1593 through 1609 removed outlier: 3.731A pdb=" N ALA A1598 " --> pdb=" O SER A1594 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS A1599 " --> pdb=" O GLY A1595 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS A1607 " --> pdb=" O PHE A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1612 through 1622 Processing helix chain 'A' and resid 1625 through 1647 removed outlier: 3.745A 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: 3.525A pdb=" N LEU A1701 " --> pdb=" O GLU A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1749 through 1768 Processing helix chain 'A' and resid 1772 through 1797 removed outlier: 3.704A pdb=" N GLU A1795 " --> pdb=" O ILE A1791 " (cutoff:3.500A) Processing helix chain 'A' and resid 1799 through 1807 removed outlier: 3.961A pdb=" N LYS A1803 " --> pdb=" O GLY A1800 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A1804 " --> pdb=" O CYS A1801 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1830 removed outlier: 4.370A pdb=" N GLU A1824 " --> pdb=" O SER A1820 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU A1825 " --> pdb=" O ARG A1821 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1845 removed outlier: 3.956A pdb=" N LEU A1839 " --> pdb=" O ASP A1835 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY A1845 " --> pdb=" O ILE A1841 " (cutoff:3.500A) Processing helix chain 'A' and resid 1846 through 1849 removed outlier: 3.647A pdb=" N LEU A1849 " --> pdb=" O ALA A1846 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1846 through 1849' 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 1907 removed outlier: 3.589A pdb=" N SER A1906 " --> pdb=" O PRO A1903 " (cutoff:3.500A) Processing helix chain 'A' and resid 1920 through 1933 removed outlier: 4.061A pdb=" N LEU A1924 " --> pdb=" O SER A1920 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A1925 " --> pdb=" O PHE A1921 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A1928 " --> pdb=" O LEU A1924 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A1933 " --> pdb=" O ILE A1929 " (cutoff:3.500A) Processing helix chain 'A' and resid 1936 through 1941 Processing helix chain 'A' and resid 1958 through 1972 removed outlier: 5.379A pdb=" N ALA A1967 " --> pdb=" O GLU A1963 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ASN A1968 " --> pdb=" O GLN A1964 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A1972 " --> pdb=" O ASN A1968 " (cutoff:3.500A) Processing helix chain 'A' and resid 1984 through 1995 Processing helix chain 'A' and resid 2011 through 2017 Processing helix chain 'A' and resid 2044 through 2052 removed outlier: 4.045A pdb=" N LYS A2048 " --> pdb=" O GLY A2044 " (cutoff:3.500A) Processing helix chain 'A' and resid 2065 through 2082 removed outlier: 3.600A pdb=" N ARG A2071 " --> pdb=" O ARG A2067 " (cutoff:3.500A) Processing helix chain 'A' and resid 2088 through 2097 removed outlier: 4.016A pdb=" N TYR A2092 " --> pdb=" O PRO A2088 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A2097 " --> pdb=" O VAL A2093 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1737 through 1742 removed outlier: 4.188A pdb=" N THR A1724 " --> pdb=" O ALA A1714 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1975 through 1979 removed outlier: 6.452A pdb=" N PHE A1949 " --> pdb=" O ILE A1999 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA A2001 " --> pdb=" O PHE A1949 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A1951 " --> pdb=" O ALA A2001 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR A1998 " --> pdb=" O LEU A2025 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N PHE A2027 " --> pdb=" O TYR A1998 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TYR A2000 " --> pdb=" O PHE A2027 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA A2024 " --> pdb=" O LEU A2058 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N ASN A2060 " --> pdb=" O ALA A2024 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N LEU A2026 " --> pdb=" O ASN A2060 " (cutoff:3.500A) 668 hydrogen bonds defined for protein. 1965 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 0.93 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: 3386 1.34 - 1.46: 1868 1.46 - 1.58: 5027 1.58 - 1.70: 0 1.70 - 1.81: 59 Bond restraints: 10340 Sorted by residual: bond pdb=" N GLY A 446 " pdb=" CA GLY A 446 " ideal model delta sigma weight residual 1.446 1.476 -0.030 1.02e-02 9.61e+03 8.71e+00 bond pdb=" N VAL A 434 " pdb=" CA VAL A 434 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.21e-02 6.83e+03 7.74e+00 bond pdb=" N VAL A 427 " pdb=" CA VAL A 427 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.68e+00 bond pdb=" N VAL A 511 " pdb=" CA VAL A 511 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.43e+00 bond pdb=" N VAL A 435 " pdb=" CA VAL A 435 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.32e+00 ... (remaining 10335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 13503 1.77 - 3.54: 513 3.54 - 5.31: 47 5.31 - 7.08: 4 7.08 - 8.84: 3 Bond angle restraints: 14070 Sorted by residual: angle pdb=" CA GLY A 446 " pdb=" C GLY A 446 " pdb=" O GLY A 446 " ideal model delta sigma weight residual 122.23 118.36 3.87 6.90e-01 2.10e+00 3.14e+01 angle pdb=" N PHE A 712 " pdb=" CA PHE A 712 " pdb=" C PHE A 712 " ideal model delta sigma weight residual 112.87 107.76 5.11 1.20e+00 6.94e-01 1.81e+01 angle pdb=" N GLU A 711 " pdb=" CA GLU A 711 " pdb=" C GLU A 711 " ideal model delta sigma weight residual 113.02 108.59 4.43 1.20e+00 6.94e-01 1.36e+01 angle pdb=" N LYS A 491 " pdb=" CA LYS A 491 " pdb=" C LYS A 491 " ideal model delta sigma weight residual 113.16 107.92 5.24 1.42e+00 4.96e-01 1.36e+01 angle pdb=" N LEU A 517 " pdb=" CA LEU A 517 " pdb=" C LEU A 517 " ideal model delta sigma weight residual 113.01 108.73 4.28 1.20e+00 6.94e-01 1.27e+01 ... (remaining 14065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 5691 17.33 - 34.66: 443 34.66 - 51.99: 97 51.99 - 69.33: 37 69.33 - 86.66: 7 Dihedral angle restraints: 6275 sinusoidal: 2377 harmonic: 3898 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 -152.14 66.14 1 1.00e+01 1.00e-02 5.72e+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 180.00 163.56 16.44 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA GLU A2074 " pdb=" CB GLU A2074 " pdb=" CG GLU A2074 " pdb=" CD GLU A2074 " ideal model delta sinusoidal sigma weight residual 180.00 120.51 59.49 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 6272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1287 0.045 - 0.090: 249 0.090 - 0.136: 103 0.136 - 0.181: 13 0.181 - 0.226: 4 Chirality restraints: 1656 Sorted by residual: chirality pdb=" CA ILE A 479 " pdb=" N ILE A 479 " pdb=" C ILE A 479 " pdb=" CB ILE A 479 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA VAL A 435 " pdb=" N VAL A 435 " pdb=" C VAL A 435 " pdb=" CB VAL A 435 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.35e-01 chirality pdb=" CA VAL A 490 " pdb=" N VAL A 490 " pdb=" C VAL A 490 " pdb=" CB VAL A 490 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.68e-01 ... (remaining 1653 not shown) Planarity restraints: 1805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A1687 " -0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A1688 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A1688 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1688 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A1683 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.02e+00 pdb=" CD GLU A1683 " 0.025 2.00e-02 2.50e+03 pdb=" OE1 GLU A1683 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU A1683 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 700 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.65e+00 pdb=" CG ASP A 700 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASP A 700 " -0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP A 700 " -0.008 2.00e-02 2.50e+03 ... (remaining 1802 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1140 2.74 - 3.28: 10003 3.28 - 3.82: 15582 3.82 - 4.36: 18896 4.36 - 4.90: 32079 Nonbonded interactions: 77700 Sorted by model distance: nonbonded pdb=" NZ LYS A 553 " pdb=" O LYS A 567 " model vdw 2.206 3.120 nonbonded pdb=" N GLN A 643 " pdb=" OE1 GLN A 643 " model vdw 2.224 3.120 nonbonded pdb=" N GLU A1867 " pdb=" OE1 GLU A1867 " model vdw 2.259 3.120 nonbonded pdb=" O THR A 568 " pdb=" OG SER A 572 " model vdw 2.260 3.040 nonbonded pdb=" O LYS A 755 " pdb=" OG1 THR A 759 " model vdw 2.271 3.040 ... (remaining 77695 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.900 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.008 0.547 10345 Z= 0.369 Angle : 0.740 25.235 14075 Z= 0.470 Chirality : 0.044 0.226 1656 Planarity : 0.004 0.036 1805 Dihedral : 13.978 86.658 3734 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.64 % Favored : 97.28 % Rotamer: Outliers : 0.28 % Allowed : 10.91 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.74 (0.23), residues: 1324 helix: 1.00 (0.17), residues: 897 sheet: 2.67 (0.77), residues: 48 loop : -0.93 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 702 TYR 0.015 0.001 TYR A 730 PHE 0.014 0.001 PHE A1139 TRP 0.012 0.001 TRP A 683 HIS 0.005 0.001 HIS A1630 Details of bonding type rmsd covalent geometry : bond 0.00474 (10340) covalent geometry : angle 0.69390 (14070) SS BOND : bond 0.00700 ( 1) SS BOND : angle 0.24337 ( 2) hydrogen bonds : bond 0.26990 ( 668) hydrogen bonds : angle 6.04992 ( 1965) metal coordination : bond 0.35339 ( 4) metal coordination : angle 17.65947 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 105 average time/residue: 0.1166 time to fit residues: 16.1305 Evaluate side-chains 101 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 809 HIS A1208 HIS A1717 GLN A1745 GLN A1764 GLN A1890 HIS A1964 GLN A1995 HIS A2078 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.056959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.043738 restraints weight = 27867.381| |-----------------------------------------------------------------------------| r_work (start): 0.2490 rms_B_bonded: 2.02 r_work: 0.2373 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2254 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10345 Z= 0.174 Angle : 0.605 9.423 14075 Z= 0.317 Chirality : 0.039 0.209 1656 Planarity : 0.004 0.040 1805 Dihedral : 4.137 16.000 1424 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.80 % Allowed : 10.25 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.69 (0.23), residues: 1324 helix: 1.90 (0.17), residues: 903 sheet: 2.53 (0.72), residues: 48 loop : -1.05 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1836 TYR 0.015 0.002 TYR A2092 PHE 0.021 0.002 PHE A 712 TRP 0.019 0.001 TRP A 683 HIS 0.007 0.001 HIS A1630 Details of bonding type rmsd covalent geometry : bond 0.00377 (10340) covalent geometry : angle 0.60147 (14070) SS BOND : bond 0.00908 ( 1) SS BOND : angle 0.73272 ( 2) hydrogen bonds : bond 0.07016 ( 668) hydrogen bonds : angle 4.40158 ( 1965) metal coordination : bond 0.01072 ( 4) metal coordination : angle 4.72210 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 ARG cc_start: 0.8352 (ttp-110) cc_final: 0.7978 (ttp-170) REVERT: A 1485 MET cc_start: 0.7537 (mmm) cc_final: 0.7265 (ptt) outliers start: 19 outliers final: 10 residues processed: 115 average time/residue: 0.1095 time to fit residues: 16.7552 Evaluate side-chains 113 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 PHE Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1145 THR Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1881 GLN Chi-restraints excluded: chain A residue 2046 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 95 optimal weight: 0.0370 chunk 117 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 80 optimal weight: 0.0050 chunk 96 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 overall best weight: 0.4072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 ASN A 918 ASN ** A1295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1749 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.058408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.044956 restraints weight = 28283.349| |-----------------------------------------------------------------------------| r_work (start): 0.2534 rms_B_bonded: 2.06 r_work: 0.2422 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2303 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10345 Z= 0.124 Angle : 0.522 9.631 14075 Z= 0.267 Chirality : 0.036 0.185 1656 Planarity : 0.004 0.042 1805 Dihedral : 3.927 16.727 1424 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.14 % Allowed : 12.43 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.10 (0.24), residues: 1324 helix: 2.26 (0.17), residues: 905 sheet: 2.62 (0.74), residues: 48 loop : -1.06 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 664 TYR 0.016 0.001 TYR A 730 PHE 0.015 0.001 PHE A 712 TRP 0.015 0.001 TRP A 683 HIS 0.004 0.001 HIS A1630 Details of bonding type rmsd covalent geometry : bond 0.00255 (10340) covalent geometry : angle 0.51781 (14070) SS BOND : bond 0.00754 ( 1) SS BOND : angle 3.57900 ( 2) hydrogen bonds : bond 0.05445 ( 668) hydrogen bonds : angle 4.01294 ( 1965) metal coordination : bond 0.01003 ( 4) metal coordination : angle 3.61653 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 ARG cc_start: 0.8214 (ttp-110) cc_final: 0.7988 (ttp80) REVERT: A 618 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.8008 (m) REVERT: A 1485 MET cc_start: 0.7510 (mmm) cc_final: 0.7276 (ptt) REVERT: A 1626 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8892 (mp) outliers start: 12 outliers final: 4 residues processed: 118 average time/residue: 0.0982 time to fit residues: 15.4047 Evaluate side-chains 111 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1626 ILE Chi-restraints excluded: chain A residue 1686 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 122 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 48 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.057259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.043805 restraints weight = 28327.659| |-----------------------------------------------------------------------------| r_work (start): 0.2501 rms_B_bonded: 2.00 r_work: 0.2389 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2269 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10345 Z= 0.147 Angle : 0.543 8.969 14075 Z= 0.276 Chirality : 0.037 0.209 1656 Planarity : 0.004 0.040 1805 Dihedral : 3.942 16.840 1424 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.99 % Allowed : 13.28 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.18 (0.24), residues: 1324 helix: 2.34 (0.17), residues: 906 sheet: 2.55 (0.73), residues: 48 loop : -1.08 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1535 TYR 0.014 0.001 TYR A2092 PHE 0.019 0.002 PHE A 712 TRP 0.017 0.001 TRP A 683 HIS 0.006 0.001 HIS A1630 Details of bonding type rmsd covalent geometry : bond 0.00335 (10340) covalent geometry : angle 0.54086 (14070) SS BOND : bond 0.01180 ( 1) SS BOND : angle 2.04890 ( 2) hydrogen bonds : bond 0.05538 ( 668) hydrogen bonds : angle 3.96436 ( 1965) metal coordination : bond 0.00538 ( 4) metal coordination : angle 3.08072 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 GLU cc_start: 0.9017 (tp30) cc_final: 0.8722 (mm-30) REVERT: A 609 ASP cc_start: 0.8685 (m-30) cc_final: 0.8454 (m-30) REVERT: A 1626 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8903 (mp) outliers start: 21 outliers final: 15 residues processed: 122 average time/residue: 0.1009 time to fit residues: 16.6218 Evaluate side-chains 119 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1145 THR Chi-restraints excluded: chain A residue 1582 SER Chi-restraints excluded: chain A residue 1626 ILE Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 1971 SER Chi-restraints excluded: chain A residue 2031 SER Chi-restraints excluded: chain A residue 2046 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 83 optimal weight: 0.3980 chunk 66 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 GLN ** A1295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.057700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.044270 restraints weight = 28205.810| |-----------------------------------------------------------------------------| r_work (start): 0.2513 rms_B_bonded: 2.01 r_work: 0.2405 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2288 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10345 Z= 0.128 Angle : 0.524 9.091 14075 Z= 0.266 Chirality : 0.037 0.191 1656 Planarity : 0.004 0.041 1805 Dihedral : 3.900 17.344 1424 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.80 % Allowed : 14.23 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.32 (0.24), residues: 1324 helix: 2.43 (0.17), residues: 907 sheet: 2.61 (0.74), residues: 48 loop : -1.00 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 664 TYR 0.014 0.001 TYR A 730 PHE 0.019 0.001 PHE A 712 TRP 0.016 0.001 TRP A 683 HIS 0.004 0.001 HIS A1630 Details of bonding type rmsd covalent geometry : bond 0.00285 (10340) covalent geometry : angle 0.52231 (14070) SS BOND : bond 0.00827 ( 1) SS BOND : angle 0.70279 ( 2) hydrogen bonds : bond 0.05077 ( 668) hydrogen bonds : angle 3.85478 ( 1965) metal coordination : bond 0.00499 ( 4) metal coordination : angle 2.70009 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1626 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8887 (mp) outliers start: 19 outliers final: 11 residues processed: 120 average time/residue: 0.1032 time to fit residues: 16.7821 Evaluate side-chains 115 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1145 THR Chi-restraints excluded: chain A residue 1582 SER Chi-restraints excluded: chain A residue 1626 ILE Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 2031 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 59 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 3 optimal weight: 20.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1635 HIS ** A2039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.056939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.043426 restraints weight = 28473.532| |-----------------------------------------------------------------------------| r_work (start): 0.2491 rms_B_bonded: 2.02 r_work: 0.2379 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2260 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10345 Z= 0.150 Angle : 0.542 8.738 14075 Z= 0.276 Chirality : 0.037 0.165 1656 Planarity : 0.004 0.040 1805 Dihedral : 3.943 17.634 1424 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.80 % Allowed : 14.80 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.24), residues: 1324 helix: 2.38 (0.17), residues: 907 sheet: 2.50 (0.73), residues: 48 loop : -1.05 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 664 TYR 0.014 0.001 TYR A2092 PHE 0.024 0.002 PHE A 712 TRP 0.017 0.001 TRP A 549 HIS 0.005 0.001 HIS A1630 Details of bonding type rmsd covalent geometry : bond 0.00349 (10340) covalent geometry : angle 0.54070 (14070) SS BOND : bond 0.00920 ( 1) SS BOND : angle 0.40647 ( 2) hydrogen bonds : bond 0.05388 ( 668) hydrogen bonds : angle 3.87483 ( 1965) metal coordination : bond 0.00454 ( 4) metal coordination : angle 2.48128 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1241 GLU cc_start: 0.8633 (tp30) cc_final: 0.8324 (tp30) REVERT: A 1626 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8917 (mp) outliers start: 19 outliers final: 15 residues processed: 116 average time/residue: 0.1057 time to fit residues: 16.6098 Evaluate side-chains 117 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1145 THR Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1191 CYS Chi-restraints excluded: chain A residue 1217 SER Chi-restraints excluded: chain A residue 1582 SER Chi-restraints excluded: chain A residue 1626 ILE Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 2031 SER Chi-restraints excluded: chain A residue 2046 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 63 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 GLN ** A1295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.056693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.043216 restraints weight = 28431.547| |-----------------------------------------------------------------------------| r_work (start): 0.2484 rms_B_bonded: 2.01 r_work: 0.2372 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2253 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10345 Z= 0.150 Angle : 0.543 8.822 14075 Z= 0.277 Chirality : 0.037 0.174 1656 Planarity : 0.004 0.040 1805 Dihedral : 3.976 18.367 1424 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.90 % Allowed : 14.90 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.23 (0.23), residues: 1324 helix: 2.38 (0.17), residues: 907 sheet: 2.52 (0.73), residues: 48 loop : -1.07 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 664 TYR 0.014 0.001 TYR A2092 PHE 0.025 0.002 PHE A 712 TRP 0.020 0.001 TRP A 549 HIS 0.005 0.001 HIS A1630 Details of bonding type rmsd covalent geometry : bond 0.00348 (10340) covalent geometry : angle 0.54196 (14070) SS BOND : bond 0.00860 ( 1) SS BOND : angle 0.32556 ( 2) hydrogen bonds : bond 0.05419 ( 668) hydrogen bonds : angle 3.85941 ( 1965) metal coordination : bond 0.00281 ( 4) metal coordination : angle 2.02853 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 ARG cc_start: 0.8427 (ttm110) cc_final: 0.8188 (ptp90) REVERT: A 587 GLU cc_start: 0.9039 (tp30) cc_final: 0.8761 (mm-30) REVERT: A 1626 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8921 (mp) outliers start: 20 outliers final: 16 residues processed: 118 average time/residue: 0.0993 time to fit residues: 15.7767 Evaluate side-chains 116 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 871 HIS Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1145 THR Chi-restraints excluded: chain A residue 1191 CYS Chi-restraints excluded: chain A residue 1217 SER Chi-restraints excluded: chain A residue 1582 SER Chi-restraints excluded: chain A residue 1626 ILE Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 2031 SER Chi-restraints excluded: chain A residue 2046 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 96 optimal weight: 0.1980 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1237 GLN A2039 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.056897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.043370 restraints weight = 28155.007| |-----------------------------------------------------------------------------| r_work (start): 0.2490 rms_B_bonded: 2.01 r_work: 0.2380 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2262 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10345 Z= 0.145 Angle : 0.574 16.168 14075 Z= 0.287 Chirality : 0.037 0.177 1656 Planarity : 0.004 0.040 1805 Dihedral : 3.994 18.816 1424 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.90 % Allowed : 15.18 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.23 (0.24), residues: 1324 helix: 2.33 (0.17), residues: 915 sheet: 2.52 (0.74), residues: 48 loop : -0.99 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 664 TYR 0.014 0.001 TYR A2092 PHE 0.022 0.002 PHE A 712 TRP 0.020 0.001 TRP A 549 HIS 0.005 0.001 HIS A1630 Details of bonding type rmsd covalent geometry : bond 0.00334 (10340) covalent geometry : angle 0.56835 (14070) SS BOND : bond 0.01289 ( 1) SS BOND : angle 6.10099 ( 2) hydrogen bonds : bond 0.05288 ( 668) hydrogen bonds : angle 3.83761 ( 1965) metal coordination : bond 0.00339 ( 4) metal coordination : angle 2.04458 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 GLU cc_start: 0.9034 (tp30) cc_final: 0.8756 (mm-30) REVERT: A 1241 GLU cc_start: 0.8676 (tp30) cc_final: 0.8461 (tp30) REVERT: A 1626 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8919 (mp) outliers start: 20 outliers final: 16 residues processed: 116 average time/residue: 0.1089 time to fit residues: 17.1591 Evaluate side-chains 115 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 871 HIS Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1145 THR Chi-restraints excluded: chain A residue 1191 CYS Chi-restraints excluded: chain A residue 1582 SER Chi-restraints excluded: chain A residue 1626 ILE Chi-restraints excluded: chain A residue 1641 SER Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1775 GLU Chi-restraints excluded: chain A residue 2031 SER Chi-restraints excluded: chain A residue 2046 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 90 optimal weight: 0.4980 chunk 87 optimal weight: 0.8980 chunk 3 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 0.0970 chunk 8 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.057597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.044126 restraints weight = 28320.329| |-----------------------------------------------------------------------------| r_work (start): 0.2513 rms_B_bonded: 2.03 r_work: 0.2404 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2285 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10345 Z= 0.123 Angle : 0.555 14.322 14075 Z= 0.278 Chirality : 0.036 0.173 1656 Planarity : 0.004 0.041 1805 Dihedral : 3.926 19.107 1424 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.80 % Allowed : 15.75 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.37 (0.24), residues: 1324 helix: 2.43 (0.17), residues: 915 sheet: 2.59 (0.75), residues: 48 loop : -0.91 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 664 TYR 0.013 0.001 TYR A2092 PHE 0.026 0.001 PHE A 712 TRP 0.023 0.001 TRP A 549 HIS 0.004 0.001 HIS A1630 Details of bonding type rmsd covalent geometry : bond 0.00278 (10340) covalent geometry : angle 0.55178 (14070) SS BOND : bond 0.00678 ( 1) SS BOND : angle 4.44182 ( 2) hydrogen bonds : bond 0.04730 ( 668) hydrogen bonds : angle 3.72427 ( 1965) metal coordination : bond 0.00348 ( 4) metal coordination : angle 1.90023 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1241 GLU cc_start: 0.8657 (tp30) cc_final: 0.8286 (tp30) REVERT: A 1626 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8903 (mp) outliers start: 19 outliers final: 15 residues processed: 114 average time/residue: 0.1046 time to fit residues: 16.2073 Evaluate side-chains 117 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 871 HIS Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1145 THR Chi-restraints excluded: chain A residue 1191 CYS Chi-restraints excluded: chain A residue 1217 SER Chi-restraints excluded: chain A residue 1582 SER Chi-restraints excluded: chain A residue 1626 ILE Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 2031 SER Chi-restraints excluded: chain A residue 2046 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 123 optimal weight: 0.0070 chunk 72 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.057051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.043659 restraints weight = 27978.740| |-----------------------------------------------------------------------------| r_work (start): 0.2498 rms_B_bonded: 2.01 r_work: 0.2388 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2268 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10345 Z= 0.140 Angle : 0.580 13.951 14075 Z= 0.294 Chirality : 0.037 0.192 1656 Planarity : 0.004 0.042 1805 Dihedral : 3.939 19.155 1424 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.71 % Allowed : 16.22 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.31 (0.24), residues: 1324 helix: 2.37 (0.17), residues: 916 sheet: 2.52 (0.74), residues: 48 loop : -0.90 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 664 TYR 0.014 0.001 TYR A2092 PHE 0.027 0.002 PHE A 712 TRP 0.025 0.001 TRP A 549 HIS 0.004 0.001 HIS A1630 Details of bonding type rmsd covalent geometry : bond 0.00324 (10340) covalent geometry : angle 0.57774 (14070) SS BOND : bond 0.00834 ( 1) SS BOND : angle 4.24735 ( 2) hydrogen bonds : bond 0.05002 ( 668) hydrogen bonds : angle 3.75069 ( 1965) metal coordination : bond 0.00368 ( 4) metal coordination : angle 1.83288 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 GLU cc_start: 0.9025 (tp30) cc_final: 0.8717 (mm-30) REVERT: A 1241 GLU cc_start: 0.8654 (tp30) cc_final: 0.8435 (tp30) REVERT: A 1626 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8901 (mp) outliers start: 18 outliers final: 17 residues processed: 115 average time/residue: 0.0885 time to fit residues: 13.9202 Evaluate side-chains 118 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 871 HIS Chi-restraints excluded: chain A residue 872 GLN Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1145 THR Chi-restraints excluded: chain A residue 1191 CYS Chi-restraints excluded: chain A residue 1217 SER Chi-restraints excluded: chain A residue 1582 SER Chi-restraints excluded: chain A residue 1626 ILE Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 2031 SER Chi-restraints excluded: chain A residue 2046 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.5980 chunk 113 optimal weight: 0.0770 chunk 131 optimal weight: 0.9990 chunk 101 optimal weight: 0.0980 chunk 125 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.058557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.045070 restraints weight = 28258.761| |-----------------------------------------------------------------------------| r_work (start): 0.2541 rms_B_bonded: 2.03 r_work: 0.2433 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2314 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10345 Z= 0.115 Angle : 0.546 13.610 14075 Z= 0.276 Chirality : 0.036 0.175 1656 Planarity : 0.004 0.042 1805 Dihedral : 3.818 20.027 1424 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.33 % Allowed : 16.60 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.24), residues: 1324 helix: 2.49 (0.17), residues: 918 sheet: 2.64 (0.75), residues: 48 loop : -0.87 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 664 TYR 0.012 0.001 TYR A2092 PHE 0.027 0.001 PHE A 712 TRP 0.025 0.001 TRP A 549 HIS 0.003 0.001 HIS A1630 Details of bonding type rmsd covalent geometry : bond 0.00259 (10340) covalent geometry : angle 0.54391 (14070) SS BOND : bond 0.00527 ( 1) SS BOND : angle 3.69099 ( 2) hydrogen bonds : bond 0.04241 ( 668) hydrogen bonds : angle 3.60836 ( 1965) metal coordination : bond 0.00367 ( 4) metal coordination : angle 1.64140 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1945.17 seconds wall clock time: 33 minutes 58.76 seconds (2038.76 seconds total)