Starting phenix.real_space_refine on Wed Feb 4 14:24:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hn4_52306/02_2026/9hn4_52306.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hn4_52306/02_2026/9hn4_52306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hn4_52306/02_2026/9hn4_52306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hn4_52306/02_2026/9hn4_52306.map" model { file = "/net/cci-nas-00/data/ceres_data/9hn4_52306/02_2026/9hn4_52306.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hn4_52306/02_2026/9hn4_52306.cif" } resolution = 2.93 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= 0.338 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1 5.49 5 S 50 5.16 5 C 6879 2.51 5 N 1908 2.21 5 O 2016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 10855 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 283 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 7, 'TRANS': 27} Chain breaks: 2 Chain: "B" Number of atoms: 10571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1424, 10571 Classifications: {'peptide': 1424} Incomplete info: {'truncation_to_alanine': 147} Link IDs: {'PCIS': 2, 'PTRANS': 67, 'TRANS': 1354} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 521 Unresolved non-hydrogen angles: 666 Unresolved non-hydrogen dihedrals: 439 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 14, 'GLU:plan': 8, 'ARG:plan': 6, 'TYR:plan': 9, 'PHE:plan': 9, 'ASP:plan': 8, 'HIS:plan': 3, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 286 Chain: "B" 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 5628 SG CYS B1146 39.251 8.511 76.017 1.00 30.00 S ATOM 5642 SG CYS B1148 41.871 11.167 75.120 1.00 73.07 S ATOM 5662 SG CYS B1151 38.759 11.634 73.873 1.00 30.00 S Time building chain proxies: 2.46, per 1000 atoms: 0.23 Number of scatterers: 10855 At special positions: 0 Unit cell: (87.5328, 92.9472, 168.749, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 50 16.00 P 1 15.00 O 2016 8.00 N 1908 7.00 C 6879 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 637 " - pdb=" SG CYS B 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: 0.89 Conformation dependent library (CDL) restraints added in 524.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B2201 " pdb="ZN ZN B2201 " - pdb=" ND1 HIS B1142 " pdb="ZN ZN B2201 " - pdb=" SG CYS B1151 " pdb="ZN ZN B2201 " - pdb=" SG CYS B1146 " pdb="ZN ZN B2201 " - pdb=" SG CYS B1148 " Number of angles added : 3 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2758 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 2 sheets defined 73.0% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'B' and resid 308 through 328 Processing helix chain 'B' and resid 332 through 351 removed outlier: 3.633A pdb=" N THR B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 380 Processing helix chain 'B' and resid 380 through 386 Processing helix chain 'B' and resid 386 through 415 Processing helix chain 'B' and resid 419 through 442 Processing helix chain 'B' and resid 446 through 470 Processing helix chain 'B' and resid 472 through 490 Proline residue: B 482 - end of helix Processing helix chain 'B' and resid 499 through 517 removed outlier: 3.517A pdb=" N GLN B 510 " --> pdb=" O CYS B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 534 Processing helix chain 'B' and resid 538 through 560 removed outlier: 3.512A pdb=" N MET B 542 " --> pdb=" O SER B 538 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU B 544 " --> pdb=" O GLU B 540 " (cutoff:3.500A) Proline residue: B 545 - end of helix Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 568 through 574 removed outlier: 3.518A pdb=" N SER B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 595 Processing helix chain 'B' and resid 599 through 614 Processing helix chain 'B' and resid 618 through 637 Processing helix chain 'B' and resid 641 through 646 Processing helix chain 'B' and resid 648 through 663 Processing helix chain 'B' and resid 669 through 704 Processing helix chain 'B' and resid 730 through 734 Processing helix chain 'B' and resid 737 through 760 removed outlier: 3.634A pdb=" N ALA B 741 " --> pdb=" O LEU B 737 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 747 " --> pdb=" O GLN B 743 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS B 760 " --> pdb=" O GLU B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 786 removed outlier: 3.620A pdb=" N THR B 772 " --> pdb=" O CYS B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 807 Processing helix chain 'B' and resid 808 through 827 Processing helix chain 'B' and resid 828 through 844 removed outlier: 3.674A pdb=" N ALA B 832 " --> pdb=" O CYS B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 871 Processing helix chain 'B' and resid 873 through 887 Processing helix chain 'B' and resid 888 through 892 Processing helix chain 'B' and resid 894 through 913 removed outlier: 3.611A pdb=" N GLN B 903 " --> pdb=" O LEU B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 929 Processing helix chain 'B' and resid 934 through 955 Processing helix chain 'B' and resid 974 through 1002 removed outlier: 3.705A pdb=" N TRP B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1022 removed outlier: 3.582A pdb=" N ALA B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1041 Processing helix chain 'B' and resid 1043 through 1064 Processing helix chain 'B' and resid 1148 through 1153 Processing helix chain 'B' and resid 1153 through 1174 Processing helix chain 'B' and resid 1179 through 1207 Proline residue: B1192 - end of helix Processing helix chain 'B' and resid 1219 through 1237 removed outlier: 3.785A pdb=" N ASN B1236 " --> pdb=" O LEU B1232 " (cutoff:3.500A) Processing helix chain 'B' and resid 1240 through 1256 removed outlier: 3.949A pdb=" N GLN B1244 " --> pdb=" O ASN B1240 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN B1248 " --> pdb=" O GLN B1244 " (cutoff:3.500A) Processing helix chain 'B' and resid 1261 through 1278 removed outlier: 3.593A pdb=" N GLY B1278 " --> pdb=" O LEU B1274 " (cutoff:3.500A) Processing helix chain 'B' and resid 1288 through 1292 Processing helix chain 'B' and resid 1572 through 1589 Processing helix chain 'B' and resid 1593 through 1609 removed outlier: 3.688A pdb=" N ALA B1598 " --> pdb=" O SER B1594 " (cutoff:3.500A) Processing helix chain 'B' and resid 1612 through 1622 Processing helix chain 'B' and resid 1625 through 1647 Processing helix chain 'B' and resid 1668 through 1678 Processing helix chain 'B' and resid 1688 through 1701 Processing helix chain 'B' and resid 1749 through 1769 removed outlier: 4.039A pdb=" N SER B1769 " --> pdb=" O LYS B1765 " (cutoff:3.500A) Processing helix chain 'B' and resid 1772 through 1797 removed outlier: 3.727A pdb=" N TRP B1776 " --> pdb=" O ASP B1772 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR B1778 " --> pdb=" O ARG B1774 " (cutoff:3.500A) Processing helix chain 'B' and resid 1803 through 1807 removed outlier: 3.700A pdb=" N LEU B1806 " --> pdb=" O LYS B1803 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1828 removed outlier: 3.995A pdb=" N GLU B1824 " --> pdb=" O SER B1820 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP B1828 " --> pdb=" O GLU B1824 " (cutoff:3.500A) Processing helix chain 'B' and resid 1835 through 1844 Processing helix chain 'B' and resid 1845 through 1849 Processing helix chain 'B' and resid 1850 through 1862 Processing helix chain 'B' and resid 1865 through 1881 Processing helix chain 'B' and resid 1903 through 1907 Processing helix chain 'B' and resid 1920 through 1933 removed outlier: 3.667A pdb=" N LEU B1924 " --> pdb=" O SER B1920 " (cutoff:3.500A) Processing helix chain 'B' and resid 1936 through 1941 Processing helix chain 'B' and resid 1959 through 1972 removed outlier: 5.518A pdb=" N ALA B1967 " --> pdb=" O GLU B1963 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASN B1968 " --> pdb=" O GLN B1964 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B1972 " --> pdb=" O ASN B1968 " (cutoff:3.500A) Processing helix chain 'B' and resid 1984 through 1994 removed outlier: 3.603A pdb=" N GLU B1990 " --> pdb=" O GLU B1986 " (cutoff:3.500A) Processing helix chain 'B' and resid 2011 through 2017 Processing helix chain 'B' and resid 2044 through 2052 removed outlier: 3.998A pdb=" N LYS B2048 " --> pdb=" O GLY B2044 " (cutoff:3.500A) Processing helix chain 'B' and resid 2066 through 2082 Processing helix chain 'B' and resid 2088 through 2097 removed outlier: 4.037A pdb=" N TYR B2092 " --> pdb=" O PRO B2088 " (cutoff:3.500A) Processing helix chain 'B' and resid 2102 through 2107 Processing sheet with id=AA1, first strand: chain 'B' and resid 1734 through 1742 removed outlier: 5.838A pdb=" N GLU B1731 " --> pdb=" O PRO B1735 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR B1724 " --> pdb=" O ALA B1714 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR B1707 " --> pdb=" O VAL B1892 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL B1894 " --> pdb=" O THR B1707 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N CYS B1709 " --> pdb=" O VAL B1894 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 1975 through 1979 removed outlier: 6.054A pdb=" N THR B1948 " --> pdb=" O ARG B1976 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL B1978 " --> pdb=" O THR B1948 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TYR B1950 " --> pdb=" O VAL B1978 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE B1949 " --> pdb=" O ILE B1999 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ALA B2001 " --> pdb=" O PHE B1949 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL B1951 " --> pdb=" O ALA B2001 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TYR B1998 " --> pdb=" O LEU B2025 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B2024 " --> pdb=" O LEU B2058 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ASN B2060 " --> pdb=" O ALA B2024 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N LEU B2026 " --> pdb=" O ASN B2060 " (cutoff:3.500A) 786 hydrogen bonds defined for protein. 2325 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: 2.06 Time building geometry restraints manager: 1.18 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: 3637 1.34 - 1.46: 1965 1.46 - 1.58: 5390 1.58 - 1.70: 1 1.70 - 1.82: 63 Bond restraints: 11056 Sorted by residual: bond pdb=" O1P SEP A 454 " pdb=" P SEP A 454 " ideal model delta sigma weight residual 1.610 1.510 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" O3P SEP A 454 " pdb=" P SEP A 454 " ideal model delta sigma weight residual 1.610 1.513 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" O2P SEP A 454 " pdb=" P SEP A 454 " ideal model delta sigma weight residual 1.610 1.514 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" N ARG B 356 " pdb=" CA ARG B 356 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.09e-02 8.42e+03 9.06e+00 bond pdb=" N PRO B1688 " pdb=" CD PRO B1688 " ideal model delta sigma weight residual 1.474 1.432 0.042 1.40e-02 5.10e+03 9.05e+00 ... (remaining 11051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 14191 2.10 - 4.21: 805 4.21 - 6.31: 48 6.31 - 8.42: 8 8.42 - 10.52: 5 Bond angle restraints: 15057 Sorted by residual: angle pdb=" N PRO B1688 " pdb=" CD PRO B1688 " pdb=" CG PRO B1688 " ideal model delta sigma weight residual 103.80 96.78 7.02 1.20e+00 6.94e-01 3.42e+01 angle pdb=" N LYS B1803 " pdb=" CA LYS B1803 " pdb=" C LYS B1803 " ideal model delta sigma weight residual 113.72 106.28 7.44 1.30e+00 5.92e-01 3.27e+01 angle pdb=" N LEU B 769 " pdb=" CA LEU B 769 " pdb=" C LEU B 769 " ideal model delta sigma weight residual 113.18 107.31 5.87 1.21e+00 6.83e-01 2.35e+01 angle pdb=" C PHE B 735 " pdb=" CA PHE B 735 " pdb=" CB PHE B 735 " ideal model delta sigma weight residual 110.90 103.48 7.42 1.58e+00 4.01e-01 2.21e+01 angle pdb=" N LEU B1805 " pdb=" CA LEU B1805 " pdb=" C LEU B1805 " ideal model delta sigma weight residual 113.20 107.79 5.41 1.21e+00 6.83e-01 2.00e+01 ... (remaining 15052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 6007 17.67 - 35.34: 505 35.34 - 53.01: 140 53.01 - 70.69: 52 70.69 - 88.36: 8 Dihedral angle restraints: 6712 sinusoidal: 2474 harmonic: 4238 Sorted by residual: dihedral pdb=" CB CYS B 637 " pdb=" SG CYS B 637 " pdb=" SG CYS B 687 " pdb=" CB CYS B 687 " ideal model delta sinusoidal sigma weight residual -86.00 -145.77 59.77 1 1.00e+01 1.00e-02 4.77e+01 dihedral pdb=" CG ARG B1966 " pdb=" CD ARG B1966 " pdb=" NE ARG B1966 " pdb=" CZ ARG B1966 " ideal model delta sinusoidal sigma weight residual 90.00 41.66 48.34 2 1.50e+01 4.44e-03 1.19e+01 dihedral pdb=" CG ARG B1162 " pdb=" CD ARG B1162 " pdb=" NE ARG B1162 " pdb=" CZ ARG B1162 " ideal model delta sinusoidal sigma weight residual -90.00 -47.01 -42.99 2 1.50e+01 4.44e-03 9.92e+00 ... (remaining 6709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1284 0.047 - 0.095: 292 0.095 - 0.142: 155 0.142 - 0.189: 33 0.189 - 0.237: 13 Chirality restraints: 1777 Sorted by residual: chirality pdb=" CA ILE A 445 " pdb=" N ILE A 445 " pdb=" C ILE A 445 " pdb=" CB ILE A 445 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CG LEU B 581 " pdb=" CB LEU B 581 " pdb=" CD1 LEU B 581 " pdb=" CD2 LEU B 581 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA VAL B2064 " pdb=" N VAL B2064 " pdb=" C VAL B2064 " pdb=" CB VAL B2064 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1774 not shown) Planarity restraints: 1941 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B1295 " 0.080 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO B1296 " -0.204 5.00e-02 4.00e+02 pdb=" CA PRO B1296 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO B1296 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO B2100 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C PRO B2100 " 0.038 2.00e-02 2.50e+03 pdb=" O PRO B2100 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG B2101 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B1850 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO B1851 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B1851 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B1851 " -0.031 5.00e-02 4.00e+02 ... (remaining 1938 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 790 2.74 - 3.28: 11261 3.28 - 3.82: 18273 3.82 - 4.36: 21593 4.36 - 4.90: 36884 Nonbonded interactions: 88801 Sorted by model distance: nonbonded pdb=" N GLU B 617 " pdb=" OE1 GLU B 617 " model vdw 2.199 3.120 nonbonded pdb=" OH TYR B1597 " pdb=" OE1 GLU B1622 " model vdw 2.216 3.040 nonbonded pdb=" O LYS B1897 " pdb=" NE2 GLN B1900 " model vdw 2.354 3.120 nonbonded pdb=" O LEU B1790 " pdb=" OG SER B1793 " model vdw 2.385 3.040 nonbonded pdb=" NH2 ARG A 427 " pdb=" O PHE B2027 " model vdw 2.389 3.120 ... (remaining 88796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.020 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.600 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:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 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 : 0.007 0.100 11061 Z= 0.499 Angle : 0.907 18.818 15062 Z= 0.648 Chirality : 0.056 0.237 1777 Planarity : 0.006 0.118 1941 Dihedral : 15.541 88.358 3951 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.73 % Allowed : 15.67 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 1.84 (0.22), residues: 1438 helix: 2.08 (0.16), residues: 978 sheet: 2.03 (0.72), residues: 48 loop : -1.06 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1966 TYR 0.021 0.002 TYR B2072 PHE 0.013 0.001 PHE B1139 TRP 0.015 0.002 TRP B 683 HIS 0.008 0.001 HIS B1749 Details of bonding type rmsd covalent geometry : bond 0.00714 (11056) covalent geometry : angle 0.89293 (15057) SS BOND : bond 0.00653 ( 1) SS BOND : angle 2.78719 ( 2) hydrogen bonds : bond 0.15165 ( 786) hydrogen bonds : angle 5.20388 ( 2325) metal coordination : bond 0.01270 ( 4) metal coordination : angle 10.91885 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 222 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 PRO cc_start: 0.8825 (Cg_endo) cc_final: 0.8609 (Cg_exo) REVERT: B 490 VAL cc_start: 0.8208 (OUTLIER) cc_final: 0.7257 (p) REVERT: B 1682 LEU cc_start: 0.8115 (mt) cc_final: 0.7882 (mp) outliers start: 8 outliers final: 0 residues processed: 227 average time/residue: 0.6560 time to fit residues: 158.5026 Evaluate side-chains 160 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 490 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.0770 chunk 77 optimal weight: 0.0570 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.0970 chunk 55 optimal weight: 0.8980 overall best weight: 0.2054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 590 GLN B 601 GLN B 672 GLN B 736 ASN B 749 GLN B 762 GLN B 784 GLN B 891 GLN B1022 GLN B1208 HIS B1244 GLN B1248 GLN B1637 HIS B1723 ASN B1767 ASN B1852 GLN ** B2060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.084450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.065281 restraints weight = 26404.120| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.19 r_work: 0.2898 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11061 Z= 0.130 Angle : 0.564 11.979 15062 Z= 0.285 Chirality : 0.036 0.234 1777 Planarity : 0.005 0.070 1941 Dihedral : 3.853 30.819 1549 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.93 % Allowed : 19.80 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 2.44 (0.22), residues: 1438 helix: 2.51 (0.16), residues: 999 sheet: 1.89 (0.76), residues: 48 loop : -0.89 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 670 TYR 0.021 0.001 TYR B 465 PHE 0.012 0.001 PHE B1139 TRP 0.013 0.001 TRP B 683 HIS 0.011 0.001 HIS B 504 Details of bonding type rmsd covalent geometry : bond 0.00283 (11056) covalent geometry : angle 0.55954 (15057) SS BOND : bond 0.00265 ( 1) SS BOND : angle 5.36183 ( 2) hydrogen bonds : bond 0.04429 ( 786) hydrogen bonds : angle 4.10270 ( 2325) metal coordination : bond 0.00487 ( 4) metal coordination : angle 2.49401 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 GLU cc_start: 0.7893 (tt0) cc_final: 0.7513 (tt0) REVERT: B 465 TYR cc_start: 0.8455 (t80) cc_final: 0.7799 (t80) REVERT: B 490 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8509 (p) REVERT: B 529 LEU cc_start: 0.8457 (mp) cc_final: 0.8248 (tp) REVERT: B 595 VAL cc_start: 0.8401 (OUTLIER) cc_final: 0.8175 (t) REVERT: B 802 VAL cc_start: 0.8973 (t) cc_final: 0.8755 (p) REVERT: B 1682 LEU cc_start: 0.8314 (mt) cc_final: 0.8037 (mp) REVERT: B 1873 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8775 (mt) REVERT: B 2063 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8039 (m-30) outliers start: 32 outliers final: 7 residues processed: 183 average time/residue: 0.6326 time to fit residues: 124.0722 Evaluate side-chains 168 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 1258 ILE Chi-restraints excluded: chain B residue 1864 THR Chi-restraints excluded: chain B residue 1873 LEU Chi-restraints excluded: chain B residue 1982 VAL Chi-restraints excluded: chain B residue 2020 CYS Chi-restraints excluded: chain B residue 2063 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 142 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 4 optimal weight: 30.0000 chunk 81 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 102 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 76 optimal weight: 0.0170 chunk 9 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN B 672 GLN B 997 HIS B1138 ASN ** B1208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.078039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.058651 restraints weight = 26168.877| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.16 r_work: 0.2698 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11061 Z= 0.185 Angle : 0.620 11.108 15062 Z= 0.315 Chirality : 0.039 0.274 1777 Planarity : 0.005 0.058 1941 Dihedral : 4.073 32.952 1549 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.57 % Allowed : 19.52 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 2.22 (0.22), residues: 1438 helix: 2.30 (0.16), residues: 1008 sheet: 1.66 (0.75), residues: 48 loop : -0.87 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1966 TYR 0.021 0.002 TYR B2104 PHE 0.023 0.002 PHE B1030 TRP 0.015 0.002 TRP B 683 HIS 0.009 0.002 HIS B1749 Details of bonding type rmsd covalent geometry : bond 0.00425 (11056) covalent geometry : angle 0.61601 (15057) SS BOND : bond 0.02401 ( 1) SS BOND : angle 6.10919 ( 2) hydrogen bonds : bond 0.05217 ( 786) hydrogen bonds : angle 4.11414 ( 2325) metal coordination : bond 0.01060 ( 4) metal coordination : angle 1.14732 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 509 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7567 (mt) REVERT: B 535 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7993 (tm-30) REVERT: B 959 LEU cc_start: 0.9103 (mt) cc_final: 0.8894 (mt) REVERT: B 1682 LEU cc_start: 0.8826 (mt) cc_final: 0.8553 (mp) REVERT: B 1868 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8430 (ttt-90) outliers start: 39 outliers final: 12 residues processed: 186 average time/residue: 0.6943 time to fit residues: 138.0229 Evaluate side-chains 157 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 1019 THR Chi-restraints excluded: chain B residue 1258 ILE Chi-restraints excluded: chain B residue 1734 SER Chi-restraints excluded: chain B residue 1868 ARG Chi-restraints excluded: chain B residue 1873 LEU Chi-restraints excluded: chain B residue 1889 SER Chi-restraints excluded: chain B residue 1978 VAL Chi-restraints excluded: chain B residue 1982 VAL Chi-restraints excluded: chain B residue 2020 CYS Chi-restraints excluded: chain B residue 2120 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 57 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 46 optimal weight: 0.0470 chunk 10 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 510 GLN ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN ** B 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1749 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.076704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.057167 restraints weight = 26456.823| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.17 r_work: 0.2668 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11061 Z= 0.188 Angle : 0.620 12.229 15062 Z= 0.314 Chirality : 0.039 0.297 1777 Planarity : 0.005 0.053 1941 Dihedral : 4.104 29.921 1548 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.67 % Allowed : 20.26 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 2.12 (0.22), residues: 1438 helix: 2.16 (0.16), residues: 1015 sheet: 1.71 (0.76), residues: 48 loop : -0.81 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1966 TYR 0.019 0.002 TYR B2072 PHE 0.017 0.002 PHE B1030 TRP 0.017 0.002 TRP B 683 HIS 0.007 0.001 HIS B1749 Details of bonding type rmsd covalent geometry : bond 0.00438 (11056) covalent geometry : angle 0.61614 (15057) SS BOND : bond 0.00593 ( 1) SS BOND : angle 5.90577 ( 2) hydrogen bonds : bond 0.05028 ( 786) hydrogen bonds : angle 4.09472 ( 2325) metal coordination : bond 0.00574 ( 4) metal coordination : angle 1.67692 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 666 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8626 (tm-30) REVERT: B 959 LEU cc_start: 0.9186 (mt) cc_final: 0.8952 (mt) REVERT: B 1046 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8039 (tp) REVERT: B 1682 LEU cc_start: 0.8953 (mt) cc_final: 0.8667 (mp) REVERT: B 1868 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8434 (ttt-90) outliers start: 40 outliers final: 12 residues processed: 170 average time/residue: 0.6126 time to fit residues: 111.5337 Evaluate side-chains 155 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1258 ILE Chi-restraints excluded: chain B residue 1734 SER Chi-restraints excluded: chain B residue 1868 ARG Chi-restraints excluded: chain B residue 1873 LEU Chi-restraints excluded: chain B residue 1889 SER Chi-restraints excluded: chain B residue 1978 VAL Chi-restraints excluded: chain B residue 1982 VAL Chi-restraints excluded: chain B residue 2020 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 81 optimal weight: 0.6980 chunk 21 optimal weight: 0.0070 chunk 113 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN B 736 ASN ** B1208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1631 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.076569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.057023 restraints weight = 26241.849| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.16 r_work: 0.2670 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11061 Z= 0.172 Angle : 0.617 11.558 15062 Z= 0.312 Chirality : 0.038 0.310 1777 Planarity : 0.005 0.050 1941 Dihedral : 4.116 29.282 1548 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.48 % Allowed : 20.26 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 2.19 (0.22), residues: 1438 helix: 2.21 (0.16), residues: 1017 sheet: 1.56 (0.76), residues: 48 loop : -0.75 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 670 TYR 0.019 0.002 TYR B 495 PHE 0.016 0.002 PHE B1030 TRP 0.018 0.002 TRP B 683 HIS 0.004 0.001 HIS B1630 Details of bonding type rmsd covalent geometry : bond 0.00399 (11056) covalent geometry : angle 0.61173 (15057) SS BOND : bond 0.00904 ( 1) SS BOND : angle 6.96697 ( 2) hydrogen bonds : bond 0.04846 ( 786) hydrogen bonds : angle 4.06727 ( 2325) metal coordination : bond 0.00535 ( 4) metal coordination : angle 1.07154 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 526 MET cc_start: 0.8662 (tpp) cc_final: 0.8369 (tpp) REVERT: B 549 TRP cc_start: 0.8398 (t-100) cc_final: 0.8176 (t-100) REVERT: B 666 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8527 (tm-30) REVERT: B 959 LEU cc_start: 0.9230 (mt) cc_final: 0.8995 (mt) REVERT: B 1046 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.7996 (tp) REVERT: B 1868 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8378 (ttt-90) outliers start: 38 outliers final: 16 residues processed: 171 average time/residue: 0.6391 time to fit residues: 117.2115 Evaluate side-chains 153 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 873 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1258 ILE Chi-restraints excluded: chain B residue 1288 PHE Chi-restraints excluded: chain B residue 1641 SER Chi-restraints excluded: chain B residue 1734 SER Chi-restraints excluded: chain B residue 1868 ARG Chi-restraints excluded: chain B residue 1873 LEU Chi-restraints excluded: chain B residue 1889 SER Chi-restraints excluded: chain B residue 1978 VAL Chi-restraints excluded: chain B residue 1982 VAL Chi-restraints excluded: chain B residue 2020 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 53 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 5 optimal weight: 8.9990 chunk 66 optimal weight: 0.0870 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 73 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN B1203 GLN ** B1208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2060 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.076549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.057023 restraints weight = 26388.281| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.17 r_work: 0.2669 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11061 Z= 0.167 Angle : 0.625 13.442 15062 Z= 0.320 Chirality : 0.038 0.320 1777 Planarity : 0.005 0.047 1941 Dihedral : 4.178 29.838 1548 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.21 % Allowed : 21.36 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 2.19 (0.22), residues: 1438 helix: 2.21 (0.16), residues: 1019 sheet: 1.46 (0.76), residues: 48 loop : -0.72 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 670 TYR 0.019 0.002 TYR B 465 PHE 0.016 0.002 PHE B1139 TRP 0.020 0.002 TRP B 683 HIS 0.003 0.001 HIS B1630 Details of bonding type rmsd covalent geometry : bond 0.00391 (11056) covalent geometry : angle 0.61856 (15057) SS BOND : bond 0.00207 ( 1) SS BOND : angle 7.44559 ( 2) hydrogen bonds : bond 0.04739 ( 786) hydrogen bonds : angle 4.05319 ( 2325) metal coordination : bond 0.00502 ( 4) metal coordination : angle 0.97760 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TRP cc_start: 0.8453 (t-100) cc_final: 0.8125 (t-100) REVERT: B 666 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8500 (tm-30) REVERT: B 959 LEU cc_start: 0.9235 (mt) cc_final: 0.8997 (mt) REVERT: B 1046 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8020 (tp) REVERT: B 1868 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8358 (ttt-90) REVERT: B 1900 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.6707 (pm20) outliers start: 35 outliers final: 17 residues processed: 163 average time/residue: 0.6324 time to fit residues: 110.5734 Evaluate side-chains 156 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 804 GLU Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 873 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1258 ILE Chi-restraints excluded: chain B residue 1641 SER Chi-restraints excluded: chain B residue 1734 SER Chi-restraints excluded: chain B residue 1850 THR Chi-restraints excluded: chain B residue 1868 ARG Chi-restraints excluded: chain B residue 1873 LEU Chi-restraints excluded: chain B residue 1889 SER Chi-restraints excluded: chain B residue 1900 GLN Chi-restraints excluded: chain B residue 1978 VAL Chi-restraints excluded: chain B residue 1982 VAL Chi-restraints excluded: chain B residue 2020 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 127 optimal weight: 0.0970 chunk 63 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 chunk 98 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN ** B1208 HIS ** 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 = 0.3235 r_free = 0.3235 target = 0.076484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.057124 restraints weight = 26292.907| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.16 r_work: 0.2671 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11061 Z= 0.162 Angle : 0.638 11.303 15062 Z= 0.322 Chirality : 0.038 0.337 1777 Planarity : 0.005 0.046 1941 Dihedral : 4.195 31.302 1548 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.93 % Allowed : 22.00 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.22), residues: 1438 helix: 2.24 (0.16), residues: 1018 sheet: 1.37 (0.77), residues: 48 loop : -0.68 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 427 TYR 0.021 0.002 TYR B 465 PHE 0.016 0.002 PHE B1139 TRP 0.018 0.002 TRP B 683 HIS 0.008 0.001 HIS B 628 Details of bonding type rmsd covalent geometry : bond 0.00377 (11056) covalent geometry : angle 0.63207 (15057) SS BOND : bond 0.00011 ( 1) SS BOND : angle 7.68356 ( 2) hydrogen bonds : bond 0.04663 ( 786) hydrogen bonds : angle 4.08453 ( 2325) metal coordination : bond 0.00409 ( 4) metal coordination : angle 0.93049 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 526 MET cc_start: 0.8585 (tpp) cc_final: 0.8301 (tpp) REVERT: B 549 TRP cc_start: 0.8473 (t-100) cc_final: 0.8140 (t-100) REVERT: B 666 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8473 (tm-30) REVERT: B 959 LEU cc_start: 0.9263 (mt) cc_final: 0.9038 (mt) REVERT: B 1046 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8007 (tp) REVERT: B 1807 LEU cc_start: 0.8729 (mm) cc_final: 0.8519 (mp) REVERT: B 1868 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8289 (ttt-90) REVERT: B 1900 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.6628 (pm20) REVERT: B 2104 TYR cc_start: 0.8167 (m-10) cc_final: 0.7966 (m-10) outliers start: 32 outliers final: 16 residues processed: 164 average time/residue: 0.6595 time to fit residues: 116.2164 Evaluate side-chains 156 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 873 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1258 ILE Chi-restraints excluded: chain B residue 1288 PHE Chi-restraints excluded: chain B residue 1734 SER Chi-restraints excluded: chain B residue 1850 THR Chi-restraints excluded: chain B residue 1868 ARG Chi-restraints excluded: chain B residue 1873 LEU Chi-restraints excluded: chain B residue 1889 SER Chi-restraints excluded: chain B residue 1900 GLN Chi-restraints excluded: chain B residue 1978 VAL Chi-restraints excluded: chain B residue 1982 VAL Chi-restraints excluded: chain B residue 2020 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 81 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 121 optimal weight: 0.0040 chunk 47 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 5 optimal weight: 0.2980 chunk 32 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN ** B1208 HIS ** 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 = 0.3250 r_free = 0.3250 target = 0.077174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.057803 restraints weight = 26473.325| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.16 r_work: 0.2694 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11061 Z= 0.145 Angle : 0.625 10.497 15062 Z= 0.316 Chirality : 0.037 0.315 1777 Planarity : 0.005 0.046 1941 Dihedral : 4.133 29.799 1548 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.66 % Allowed : 22.73 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 2.35 (0.22), residues: 1438 helix: 2.31 (0.16), residues: 1021 sheet: 1.38 (0.77), residues: 48 loop : -0.61 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 670 TYR 0.022 0.002 TYR B 465 PHE 0.014 0.001 PHE B1139 TRP 0.020 0.002 TRP B1294 HIS 0.003 0.001 HIS B 943 Details of bonding type rmsd covalent geometry : bond 0.00335 (11056) covalent geometry : angle 0.61929 (15057) SS BOND : bond 0.00222 ( 1) SS BOND : angle 6.99423 ( 2) hydrogen bonds : bond 0.04372 ( 786) hydrogen bonds : angle 4.01586 ( 2325) metal coordination : bond 0.00228 ( 4) metal coordination : angle 0.98727 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 526 MET cc_start: 0.8655 (tpp) cc_final: 0.8321 (tpp) REVERT: B 549 TRP cc_start: 0.8464 (t-100) cc_final: 0.8148 (t-100) REVERT: B 666 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8426 (tm-30) REVERT: B 698 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8181 (mp0) REVERT: B 959 LEU cc_start: 0.9280 (mt) cc_final: 0.9067 (mt) REVERT: B 1682 LEU cc_start: 0.8932 (mt) cc_final: 0.8605 (mp) REVERT: B 1868 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8305 (ttt-90) REVERT: B 1900 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.6690 (pm20) outliers start: 29 outliers final: 16 residues processed: 159 average time/residue: 0.6674 time to fit residues: 113.9521 Evaluate side-chains 157 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 873 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1258 ILE Chi-restraints excluded: chain B residue 1641 SER Chi-restraints excluded: chain B residue 1734 SER Chi-restraints excluded: chain B residue 1850 THR Chi-restraints excluded: chain B residue 1868 ARG Chi-restraints excluded: chain B residue 1873 LEU Chi-restraints excluded: chain B residue 1889 SER Chi-restraints excluded: chain B residue 1900 GLN Chi-restraints excluded: chain B residue 1978 VAL Chi-restraints excluded: chain B residue 1982 VAL Chi-restraints excluded: chain B residue 2020 CYS Chi-restraints excluded: chain B residue 2046 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 85 optimal weight: 0.3980 chunk 128 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 4 optimal weight: 30.0000 chunk 81 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 26 optimal weight: 0.0870 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN ** B1208 HIS ** 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 = 0.3253 r_free = 0.3253 target = 0.077374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.058035 restraints weight = 26281.040| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.15 r_work: 0.2694 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11061 Z= 0.144 Angle : 0.620 10.784 15062 Z= 0.316 Chirality : 0.037 0.311 1777 Planarity : 0.005 0.045 1941 Dihedral : 4.100 28.914 1548 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.93 % Allowed : 22.82 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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: 2.43 (0.22), residues: 1438 helix: 2.35 (0.16), residues: 1022 sheet: 1.39 (0.77), residues: 48 loop : -0.54 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 427 TYR 0.022 0.002 TYR B 495 PHE 0.014 0.001 PHE B1139 TRP 0.023 0.002 TRP B1294 HIS 0.005 0.001 HIS B 628 Details of bonding type rmsd covalent geometry : bond 0.00330 (11056) covalent geometry : angle 0.61488 (15057) SS BOND : bond 0.00306 ( 1) SS BOND : angle 6.69501 ( 2) hydrogen bonds : bond 0.04346 ( 786) hydrogen bonds : angle 3.98303 ( 2325) metal coordination : bond 0.00230 ( 4) metal coordination : angle 0.92531 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 549 TRP cc_start: 0.8466 (t-100) cc_final: 0.8169 (t-100) REVERT: B 666 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8387 (tm-30) REVERT: B 698 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8255 (mp0) REVERT: B 959 LEU cc_start: 0.9285 (mt) cc_final: 0.9070 (mt) REVERT: B 1046 LEU cc_start: 0.8366 (tt) cc_final: 0.7972 (tp) REVERT: B 1233 GLU cc_start: 0.7961 (tp30) cc_final: 0.7741 (tp30) REVERT: B 1682 LEU cc_start: 0.8920 (mt) cc_final: 0.8599 (mp) REVERT: B 1780 ARG cc_start: 0.8635 (mmm160) cc_final: 0.8341 (mtt-85) REVERT: B 1868 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8332 (ttt-90) REVERT: B 1900 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.6693 (pm20) outliers start: 32 outliers final: 16 residues processed: 162 average time/residue: 0.6681 time to fit residues: 116.1194 Evaluate side-chains 156 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 666 GLU Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 873 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1258 ILE Chi-restraints excluded: chain B residue 1641 SER Chi-restraints excluded: chain B residue 1734 SER Chi-restraints excluded: chain B residue 1850 THR Chi-restraints excluded: chain B residue 1868 ARG Chi-restraints excluded: chain B residue 1873 LEU Chi-restraints excluded: chain B residue 1889 SER Chi-restraints excluded: chain B residue 1900 GLN Chi-restraints excluded: chain B residue 1978 VAL Chi-restraints excluded: chain B residue 1982 VAL Chi-restraints excluded: chain B residue 2020 CYS Chi-restraints excluded: chain B residue 2046 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 83 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 116 optimal weight: 0.0980 chunk 125 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN B 672 GLN B 743 GLN ** B1208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.077191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.057663 restraints weight = 26132.238| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.15 r_work: 0.2687 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11061 Z= 0.158 Angle : 0.676 12.745 15062 Z= 0.340 Chirality : 0.038 0.356 1777 Planarity : 0.005 0.045 1941 Dihedral : 4.159 34.791 1548 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.29 % Allowed : 23.28 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 2.41 (0.22), residues: 1438 helix: 2.36 (0.16), residues: 1018 sheet: 1.38 (0.77), residues: 48 loop : -0.57 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 427 TYR 0.019 0.002 TYR B 911 PHE 0.014 0.001 PHE B1139 TRP 0.027 0.002 TRP B1294 HIS 0.006 0.001 HIS B 628 Details of bonding type rmsd covalent geometry : bond 0.00367 (11056) covalent geometry : angle 0.66910 (15057) SS BOND : bond 0.00521 ( 1) SS BOND : angle 8.11581 ( 2) hydrogen bonds : bond 0.04512 ( 786) hydrogen bonds : angle 4.06041 ( 2325) metal coordination : bond 0.00391 ( 4) metal coordination : angle 0.86083 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 549 TRP cc_start: 0.8479 (t-100) cc_final: 0.8177 (t-100) REVERT: B 698 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8274 (mp0) REVERT: B 959 LEU cc_start: 0.9268 (mt) cc_final: 0.9052 (mt) REVERT: B 1046 LEU cc_start: 0.8380 (tt) cc_final: 0.7918 (tp) REVERT: B 1233 GLU cc_start: 0.8019 (tp30) cc_final: 0.7818 (tp30) REVERT: B 1682 LEU cc_start: 0.8963 (mt) cc_final: 0.8648 (mp) REVERT: B 1780 ARG cc_start: 0.8650 (mmm160) cc_final: 0.8351 (mtt-85) REVERT: B 1868 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8394 (ttt-90) REVERT: B 1900 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.6666 (pm20) outliers start: 25 outliers final: 17 residues processed: 158 average time/residue: 0.6644 time to fit residues: 112.7538 Evaluate side-chains 155 residues out of total 1238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 698 GLU Chi-restraints excluded: chain B residue 735 PHE Chi-restraints excluded: chain B residue 759 THR Chi-restraints excluded: chain B residue 766 VAL Chi-restraints excluded: chain B residue 873 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1258 ILE Chi-restraints excluded: chain B residue 1641 SER Chi-restraints excluded: chain B residue 1693 GLU Chi-restraints excluded: chain B residue 1734 SER Chi-restraints excluded: chain B residue 1850 THR Chi-restraints excluded: chain B residue 1868 ARG Chi-restraints excluded: chain B residue 1873 LEU Chi-restraints excluded: chain B residue 1889 SER Chi-restraints excluded: chain B residue 1900 GLN Chi-restraints excluded: chain B residue 1978 VAL Chi-restraints excluded: chain B residue 1982 VAL Chi-restraints excluded: chain B residue 2020 CYS Chi-restraints excluded: chain B residue 2046 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 83 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 128 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN ** B1208 HIS ** 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 = 0.3210 r_free = 0.3210 target = 0.075282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.055855 restraints weight = 26298.564| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 2.14 r_work: 0.2639 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11061 Z= 0.209 Angle : 0.727 13.036 15062 Z= 0.366 Chirality : 0.041 0.373 1777 Planarity : 0.005 0.046 1941 Dihedral : 4.367 36.854 1548 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.38 % Allowed : 23.37 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 2.22 (0.22), residues: 1438 helix: 2.24 (0.16), residues: 1013 sheet: 1.31 (0.77), residues: 48 loop : -0.68 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 427 TYR 0.022 0.002 TYR B 465 PHE 0.021 0.002 PHE B1030 TRP 0.030 0.002 TRP B1294 HIS 0.005 0.001 HIS B 628 Details of bonding type rmsd covalent geometry : bond 0.00498 (11056) covalent geometry : angle 0.72028 (15057) SS BOND : bond 0.00355 ( 1) SS BOND : angle 8.59044 ( 2) hydrogen bonds : bond 0.05228 ( 786) hydrogen bonds : angle 4.19284 ( 2325) metal coordination : bond 0.01093 ( 4) metal coordination : angle 1.00296 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4333.01 seconds wall clock time: 74 minutes 35.01 seconds (4475.01 seconds total)