Starting phenix.real_space_refine on Fri Oct 23 03:15:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yc8_72762/10_2026/9yc8_72762.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yc8_72762/10_2026/9yc8_72762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yc8_72762/10_2026/9yc8_72762.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yc8_72762/10_2026/9yc8_72762.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yc8_72762/10_2026/9yc8_72762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yc8_72762/10_2026/9yc8_72762.map" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 Mg 1 5.21 5 S 38 5.16 5 C 4998 2.51 5 N 1360 2.21 5 O 1425 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7822 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 7821 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1051, 7812 Classifications: {'peptide': 1051} Incomplete info: {'truncation_to_alanine': 166} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 1004} Chain breaks: 15 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 601 Unresolved non-hydrogen angles: 754 Unresolved non-hydrogen dihedrals: 491 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 12, 'TRP:plan': 1, 'ASN:plan1': 8, 'ARG:plan': 12, 'TYR:plan': 4, 'GLU:plan': 20, 'PHE:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 317 Conformer: "B" Number of residues, atoms: 1051, 7812 Classifications: {'peptide': 1051} Incomplete info: {'truncation_to_alanine': 166} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 1004} Chain breaks: 15 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 601 Unresolved non-hydrogen angles: 754 Unresolved non-hydrogen dihedrals: 491 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 12, 'TRP:plan': 1, 'ASN:plan1': 8, 'ARG:plan': 12, 'TYR:plan': 4, 'GLU:plan': 20, 'PHE:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 317 bond proxies already assigned to first conformer: 7938 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS B1347 " occ=0.45 ... (16 atoms not shown) pdb=" NZ BLYS B1347 " occ=0.55 Time building chain proxies: 3.05, per 1000 atoms: 0.39 Number of scatterers: 7822 At special positions: 0 Unit cell: (78.54, 92.565, 149.6, 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) S 38 16.00 Mg 1 11.99 O 1425 8.00 N 1360 7.00 C 4998 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 422.3 milliseconds 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 17 sheets defined 26.7% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'B' and resid 1436 through 1440 removed outlier: 3.585A pdb=" N ALA B1440 " --> pdb=" O ASN B1437 " (cutoff:3.500A) Processing helix chain 'B' and resid 1468 through 1473 Processing helix chain 'B' and resid 1496 through 1508 removed outlier: 3.556A pdb=" N LEU B1500 " --> pdb=" O ALA B1496 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER B1508 " --> pdb=" O ILE B1504 " (cutoff:3.500A) Processing helix chain 'B' and resid 1569 through 1574 removed outlier: 4.453A pdb=" N HIS B1574 " --> pdb=" O PRO B1570 " (cutoff:3.500A) Processing helix chain 'B' and resid 1602 through 1609 removed outlier: 4.386A pdb=" N ALA B1608 " --> pdb=" O CYS B1604 " (cutoff:3.500A) Processing helix chain 'B' and resid 1626 through 1630 removed outlier: 3.564A pdb=" N ASP B1630 " --> pdb=" O SER B1627 " (cutoff:3.500A) Processing helix chain 'B' and resid 1633 through 1638 removed outlier: 4.142A pdb=" N LYS B1638 " --> pdb=" O PHE B1634 " (cutoff:3.500A) Processing helix chain 'B' and resid 1642 through 1644 No H-bonds generated for 'chain 'B' and resid 1642 through 1644' Processing helix chain 'B' and resid 1645 through 1656 removed outlier: 3.520A pdb=" N PHE B1650 " --> pdb=" O MET B1646 " (cutoff:3.500A) Processing helix chain 'B' and resid 1704 through 1709 Processing helix chain 'B' and resid 1710 through 1713 Processing helix chain 'B' and resid 1770 through 1792 removed outlier: 3.741A pdb=" N CYS B1774 " --> pdb=" O CYS B1770 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE B1775 " --> pdb=" O ARG B1771 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU B1789 " --> pdb=" O ASP B1785 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B1790 " --> pdb=" O SER B1786 " (cutoff:3.500A) Processing helix chain 'B' and resid 1826 through 1835 removed outlier: 3.617A pdb=" N GLU B1835 " --> pdb=" O MET B1831 " (cutoff:3.500A) Processing helix chain 'B' and resid 1851 through 1855 Processing helix chain 'B' and resid 1913 through 1922 removed outlier: 3.809A pdb=" N LEU B1917 " --> pdb=" O SER B1913 " (cutoff:3.500A) Processing helix chain 'B' and resid 1954 through 1962 removed outlier: 3.583A pdb=" N LEU B1958 " --> pdb=" O SER B1954 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN B1960 " --> pdb=" O ASP B1956 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B1961 " --> pdb=" O ARG B1957 " (cutoff:3.500A) Processing helix chain 'B' and resid 1963 through 1966 Processing helix chain 'B' and resid 1970 through 1988 Processing helix chain 'B' and resid 1996 through 1998 No H-bonds generated for 'chain 'B' and resid 1996 through 1998' Processing helix chain 'B' and resid 2040 through 2045 removed outlier: 3.603A pdb=" N ALA B2044 " --> pdb=" O ALA B2040 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG B2045 " --> pdb=" O PRO B2041 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2040 through 2045' Processing helix chain 'B' and resid 2052 through 2068 removed outlier: 4.041A pdb=" N VAL B2056 " --> pdb=" O GLN B2052 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR B2057 " --> pdb=" O GLN B2053 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B2058 " --> pdb=" O ALA B2054 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU B2067 " --> pdb=" O LEU B2063 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR B2068 " --> pdb=" O TYR B2064 " (cutoff:3.500A) Processing helix chain 'B' and resid 2070 through 2078 removed outlier: 3.937A pdb=" N LYS B2078 " --> pdb=" O VAL B2074 " (cutoff:3.500A) Processing helix chain 'B' and resid 2081 through 2086 removed outlier: 3.894A pdb=" N GLU B2085 " --> pdb=" O ASN B2081 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2099 removed outlier: 3.916A pdb=" N GLU B2098 " --> pdb=" O ASP B2094 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR B2099 " --> pdb=" O PRO B2095 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2094 through 2099' Processing helix chain 'B' and resid 2105 through 2115 Processing helix chain 'B' and resid 2118 through 2122 removed outlier: 3.693A pdb=" N GLU B2121 " --> pdb=" O ASN B2118 " (cutoff:3.500A) Processing helix chain 'B' and resid 2124 through 2134 removed outlier: 3.599A pdb=" N SER B2134 " --> pdb=" O ASP B2130 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2139 removed outlier: 3.865A pdb=" N CYS B2139 " --> pdb=" O ALA B2135 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2135 through 2139' Processing helix chain 'B' and resid 2276 through 2280 removed outlier: 3.513A pdb=" N THR B2279 " --> pdb=" O GLU B2276 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL B2280 " --> pdb=" O ASP B2277 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2276 through 2280' Processing helix chain 'B' and resid 2346 through 2351 removed outlier: 3.849A pdb=" N SER B2350 " --> pdb=" O TYR B2346 " (cutoff:3.500A) Processing helix chain 'B' and resid 2389 through 2396 Processing helix chain 'B' and resid 2499 through 2521 removed outlier: 4.013A pdb=" N GLN B2505 " --> pdb=" O PRO B2501 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS B2509 " --> pdb=" O GLN B2505 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG B2514 " --> pdb=" O HIS B2510 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B2516 " --> pdb=" O GLU B2512 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU B2519 " --> pdb=" O LYS B2515 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N MET B2521 " --> pdb=" O LEU B2517 " (cutoff:3.500A) Processing helix chain 'B' and resid 2522 through 2527 removed outlier: 3.992A pdb=" N VAL B2526 " --> pdb=" O ARG B2522 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B2527 " --> pdb=" O ARG B2523 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2522 through 2527' Processing sheet with id=AA1, first strand: chain 'B' and resid 1337 through 1338 removed outlier: 6.986A pdb=" N LEU B1337 " --> pdb=" O TRP B1393 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 1417 through 1418 removed outlier: 6.100A pdb=" N ALA B1417 " --> pdb=" O VAL B1450 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 1690 through 1691 removed outlier: 3.549A pdb=" N VAL B1767 " --> pdb=" O ILE B1691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1761 through 1762 removed outlier: 3.956A pdb=" N LYS B1809 " --> pdb=" O GLU B1696 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1737 through 1740 removed outlier: 3.533A pdb=" N CYS B1748 " --> pdb=" O LEU B1740 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1812 through 1814 Processing sheet with id=AA7, first strand: chain 'B' and resid 1840 through 1841 Processing sheet with id=AA8, first strand: chain 'B' and resid 1893 through 1898 removed outlier: 3.913A pdb=" N ALA B1937 " --> pdb=" O VAL B1946 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 2000 through 2002 Processing sheet with id=AB1, first strand: chain 'B' and resid 2140 through 2145 removed outlier: 6.162A pdb=" N LEU B2140 " --> pdb=" O ASP B2497 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ASP B2497 " --> pdb=" O LEU B2140 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B2142 " --> pdb=" O VAL B2495 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LYS B2467 " --> pdb=" O LEU B2463 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU B2463 " --> pdb=" O LYS B2467 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N MET B2459 " --> pdb=" O LEU B2471 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 2155 through 2157 removed outlier: 6.723A pdb=" N GLY B2177 " --> pdb=" O VAL B2194 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 2199 through 2203 removed outlier: 3.538A pdb=" N CYS B2201 " --> pdb=" O GLY B2218 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR B2219 " --> pdb=" O THR B2223 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR B2223 " --> pdb=" O THR B2219 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU B2224 " --> pdb=" O LEU B2238 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 2245 through 2248 removed outlier: 3.642A pdb=" N CYS B2247 " --> pdb=" O GLY B2266 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 2271 through 2272 Processing sheet with id=AB6, first strand: chain 'B' and resid 2300 through 2302 removed outlier: 3.988A pdb=" N CYS B2302 " --> pdb=" O GLY B2318 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY B2318 " --> pdb=" O CYS B2302 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 2354 through 2358 removed outlier: 7.633A pdb=" N ALA B2366 " --> pdb=" O ILE B2355 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N VAL B2357 " --> pdb=" O TYR B2364 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N TYR B2364 " --> pdb=" O VAL B2357 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY B2385 " --> pdb=" O VAL B2375 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 2414 through 2419 removed outlier: 4.784A pdb=" N ARG B2446 " --> pdb=" O LEU B2436 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP B2438 " --> pdb=" O LEU B2444 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU B2444 " --> pdb=" O ASP B2438 " (cutoff:3.500A) 205 hydrogen bonds defined for protein. 546 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: 1.32 Time building geometry restraints manager: 0.88 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: 2556 1.34 - 1.46: 1563 1.46 - 1.58: 3783 1.58 - 1.70: 0 1.70 - 1.82: 56 Bond restraints: 7958 Sorted by residual: bond pdb=" CA ASN B1909 " pdb=" CB ASN B1909 " ideal model delta sigma weight residual 1.518 1.547 -0.029 2.08e-02 2.31e+03 1.97e+00 bond pdb=" CA ARG B1993 " pdb=" CB ARG B1993 " ideal model delta sigma weight residual 1.530 1.553 -0.022 1.69e-02 3.50e+03 1.75e+00 bond pdb=" CB ASN B1909 " pdb=" CG ASN B1909 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.53e+00 bond pdb=" CA GLU B1399 " pdb=" CB GLU B1399 " ideal model delta sigma weight residual 1.532 1.550 -0.018 1.51e-02 4.39e+03 1.48e+00 bond pdb=" C HIS B1758 " pdb=" N PRO B1759 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.41e+00 ... (remaining 7953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 10526 2.49 - 4.98: 233 4.98 - 7.47: 37 7.47 - 9.96: 10 9.96 - 12.46: 2 Bond angle restraints: 10808 Sorted by residual: angle pdb=" N ILE B1658 " pdb=" CA ILE B1658 " pdb=" C ILE B1658 " ideal model delta sigma weight residual 113.71 108.90 4.81 9.50e-01 1.11e+00 2.56e+01 angle pdb=" C TYR B1992 " pdb=" N ARG B1993 " pdb=" CA ARG B1993 " ideal model delta sigma weight residual 121.54 130.77 -9.23 1.91e+00 2.74e-01 2.34e+01 angle pdb=" CA GLU B1399 " pdb=" CB GLU B1399 " pdb=" CG GLU B1399 " ideal model delta sigma weight residual 114.10 122.95 -8.85 2.00e+00 2.50e-01 1.96e+01 angle pdb=" C PHE B1908 " pdb=" N ASN B1909 " pdb=" CA ASN B1909 " ideal model delta sigma weight residual 121.76 130.51 -8.75 2.19e+00 2.09e-01 1.60e+01 angle pdb=" C LEU B1870 " pdb=" N ASN B1871 " pdb=" CA ASN B1871 " ideal model delta sigma weight residual 121.54 128.74 -7.20 1.91e+00 2.74e-01 1.42e+01 ... (remaining 10803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4344 17.83 - 35.67: 360 35.67 - 53.50: 50 53.50 - 71.33: 11 71.33 - 89.17: 6 Dihedral angle restraints: 4771 sinusoidal: 1717 harmonic: 3054 Sorted by residual: dihedral pdb=" CA GLN B1823 " pdb=" C GLN B1823 " pdb=" N LYS B1824 " pdb=" CA LYS B1824 " ideal model delta harmonic sigma weight residual 180.00 -158.10 -21.90 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA GLU B1599 " pdb=" C GLU B1599 " pdb=" N PRO B1600 " pdb=" CA PRO B1600 " ideal model delta harmonic sigma weight residual 180.00 158.21 21.79 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA TYR B1992 " pdb=" C TYR B1992 " pdb=" N ARG B1993 " pdb=" CA ARG B1993 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 4768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 908 0.049 - 0.097: 290 0.097 - 0.146: 79 0.146 - 0.194: 9 0.194 - 0.243: 1 Chirality restraints: 1287 Sorted by residual: chirality pdb=" CB VAL B1447 " pdb=" CA VAL B1447 " pdb=" CG1 VAL B1447 " pdb=" CG2 VAL B1447 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE B2227 " pdb=" CA ILE B2227 " pdb=" CG1 ILE B2227 " pdb=" CG2 ILE B2227 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.82e-01 chirality pdb=" CA GLU B1399 " pdb=" N GLU B1399 " pdb=" C GLU B1399 " pdb=" CB GLU B1399 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.77e-01 ... (remaining 1284 not shown) Planarity restraints: 1369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B2118 " -0.055 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO B2119 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B2119 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B2119 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B1405 " 0.051 5.00e-02 4.00e+02 7.68e-02 9.45e+00 pdb=" N PRO B1406 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B1406 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B1406 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B1856 " -0.047 5.00e-02 4.00e+02 7.00e-02 7.85e+00 pdb=" N PRO B1857 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B1857 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B1857 " -0.039 5.00e-02 4.00e+02 ... (remaining 1366 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 202 2.69 - 3.24: 7509 3.24 - 3.80: 11628 3.80 - 4.35: 14591 4.35 - 4.90: 24003 Nonbonded interactions: 57933 Sorted by model distance: nonbonded pdb=" N BLYS B1347 " pdb="MG MG B2601 " model vdw 2.141 2.250 nonbonded pdb=" N ALYS B1347 " pdb="MG MG B2601 " model vdw 2.172 2.250 nonbonded pdb=" O ARG B2522 " pdb=" OG SER B2525 " model vdw 2.209 3.040 nonbonded pdb=" OG SER B1403 " pdb=" O GLN B1657 " model vdw 2.228 3.040 nonbonded pdb=" OG SER B1688 " pdb=" OE1 GLU B1689 " model vdw 2.238 3.040 ... (remaining 57928 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.860 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7958 Z= 0.163 Angle : 0.892 12.455 10808 Z= 0.447 Chirality : 0.051 0.243 1287 Planarity : 0.007 0.083 1369 Dihedral : 13.914 89.168 2781 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.48 % Favored : 88.32 % Rotamer: Outliers : 0.26 % Allowed : 0.00 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.72 (0.25), residues: 1022 helix: -2.09 (0.33), residues: 197 sheet: -1.57 (0.41), residues: 164 loop : -1.84 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1483 TYR 0.025 0.002 TYR B1898 PHE 0.015 0.001 PHE B1704 TRP 0.046 0.004 TRP B1705 HIS 0.005 0.001 HIS B1977 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 7958) covalent geometry : angle 0.89242 / 0.45 (10808) hydrogen bonds : bond 0.20647 / 14.51 ( 205) hydrogen bonds : angle 8.78262 / 5.95 ( 546) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 2109 LYS cc_start: 0.9294 (mmpt) cc_final: 0.8990 (mmmt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.0681 time to fit residues: 10.8217 Evaluate side-chains 80 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 100, 38, 61] chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0030 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1928 HIS ** B2127 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 = 0.4220 r_free = 0.4220 target = 0.138813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.108160 restraints weight = 32960.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.108692 restraints weight = 20360.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.110253 restraints weight = 15850.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.110866 restraints weight = 12017.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.111313 restraints weight = 11397.170| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7958 Z= 0.137 Angle : 0.663 8.730 10808 Z= 0.335 Chirality : 0.045 0.144 1287 Planarity : 0.005 0.066 1369 Dihedral : 4.930 21.218 1105 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.91 % Favored : 89.89 % Rotamer: Outliers : 0.26 % Allowed : 3.25 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.39 (0.26), residues: 1022 helix: -1.60 (0.34), residues: 221 sheet: -1.12 (0.46), residues: 129 loop : -1.75 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1707 TYR 0.018 0.002 TYR B1992 PHE 0.009 0.001 PHE B1408 TRP 0.028 0.002 TRP B1705 HIS 0.011 0.001 HIS B1977 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 7958) covalent geometry : angle 0.66320 / 0.34 (10808) hydrogen bonds : bond 0.04033 / 2.78 ( 205) hydrogen bonds : angle 6.26391 / 4.30 ( 546) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1992 TYR cc_start: 0.8411 (t80) cc_final: 0.8042 (t80) REVERT: B 2426 TRP cc_start: 0.7816 (m-10) cc_final: 0.7506 (m-10) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.0655 time to fit residues: 11.6776 Evaluate side-chains 84 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [13, 68, 50, 34, 80, 25, 102, 23, 56, 57, 58] chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 30.0000 chunk 25 optimal weight: 1.9990 chunk 102 optimal weight: 0.0770 chunk 23 optimal weight: 0.0270 chunk 56 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.144225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.114921 restraints weight = 38329.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.116903 restraints weight = 27528.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.119000 restraints weight = 17199.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.119852 restraints weight = 12423.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.120346 restraints weight = 11273.012| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3962 r_free = 0.3962 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3962 r_free = 0.3962 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7958 Z= 0.113 Angle : 0.632 9.802 10808 Z= 0.316 Chirality : 0.045 0.140 1287 Planarity : 0.005 0.063 1369 Dihedral : 4.704 21.460 1105 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.81 % Favored : 89.99 % Rotamer: Outliers : 0.26 % Allowed : 1.56 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.30 (0.26), residues: 1022 helix: -1.18 (0.36), residues: 217 sheet: -1.60 (0.40), residues: 159 loop : -1.68 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1707 TYR 0.021 0.001 TYR B1992 PHE 0.009 0.001 PHE B1641 TRP 0.022 0.002 TRP B1705 HIS 0.004 0.001 HIS B1928 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 7958) covalent geometry : angle 0.63241 / 0.32 (10808) hydrogen bonds : bond 0.03442 / 2.39 ( 205) hydrogen bonds : angle 5.74776 / 3.96 ( 546) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: B 1709 ILE cc_start: 0.7185 (mm) cc_final: 0.6893 (mm) REVERT: B 2104 TRP cc_start: 0.7682 (t-100) cc_final: 0.6958 (t-100) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.0665 time to fit residues: 12.2086 Evaluate side-chains 90 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [100, 51, 61, 71, 1, 50, 57, 29, 101, 103, 85] chunk 100 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 1 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 29 optimal weight: 0.0370 chunk 101 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1571 HIS ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2510 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 = 0.4319 r_free = 0.4319 target = 0.144070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.114963 restraints weight = 41267.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.116431 restraints weight = 29340.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.118831 restraints weight = 18523.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.119804 restraints weight = 12822.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.120361 restraints weight = 11612.299| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3959 r_free = 0.3959 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3959 r_free = 0.3959 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7958 Z= 0.111 Angle : 0.616 8.117 10808 Z= 0.308 Chirality : 0.045 0.145 1287 Planarity : 0.005 0.057 1369 Dihedral : 4.586 20.163 1105 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.21 % Favored : 89.60 % Rotamer: Outliers : 0.26 % Allowed : 2.08 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.26), residues: 1022 helix: -1.13 (0.35), residues: 223 sheet: -1.72 (0.39), residues: 166 loop : -1.71 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1707 TYR 0.017 0.001 TYR B1992 PHE 0.007 0.001 PHE B2129 TRP 0.024 0.002 TRP B2426 HIS 0.004 0.001 HIS B1928 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 7958) covalent geometry : angle 0.61607 / 0.31 (10808) hydrogen bonds : bond 0.03179 / 2.20 ( 205) hydrogen bonds : angle 5.53578 / 3.80 ( 546) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 1709 ILE cc_start: 0.7145 (mm) cc_final: 0.6888 (mm) REVERT: B 1931 SER cc_start: 0.7471 (p) cc_final: 0.7269 (p) REVERT: B 1991 ILE cc_start: 0.8885 (pt) cc_final: 0.8526 (mt) REVERT: B 1992 TYR cc_start: 0.8148 (t80) cc_final: 0.7825 (t80) REVERT: B 2104 TRP cc_start: 0.7758 (t-100) cc_final: 0.7096 (t-100) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0618 time to fit residues: 11.6227 Evaluate side-chains 90 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [47, 23, 99, 32, 34, 76, 54, 70, 84, 13, 101] chunk 47 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.141258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.110305 restraints weight = 31431.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.110867 restraints weight = 20613.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.112147 restraints weight = 16266.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.112543 restraints weight = 13864.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.112837 restraints weight = 12637.042| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3825 r_free = 0.3825 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3825 r_free = 0.3825 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7958 Z= 0.158 Angle : 0.658 7.359 10808 Z= 0.333 Chirality : 0.045 0.147 1287 Planarity : 0.005 0.055 1369 Dihedral : 4.791 21.600 1105 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.70 % Favored : 89.11 % Rotamer: Outliers : 0.26 % Allowed : 1.04 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.26), residues: 1022 helix: -1.02 (0.35), residues: 223 sheet: -1.74 (0.39), residues: 166 loop : -1.70 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1707 TYR 0.020 0.002 TYR B2018 PHE 0.010 0.001 PHE B1792 TRP 0.047 0.002 TRP B2426 HIS 0.006 0.001 HIS B1928 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 7958) covalent geometry : angle 0.65771 / 0.33 (10808) hydrogen bonds : bond 0.03302 / 2.24 ( 205) hydrogen bonds : angle 5.54337 / 3.78 ( 546) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: B 1709 ILE cc_start: 0.7327 (mm) cc_final: 0.7095 (mm) REVERT: B 1991 ILE cc_start: 0.8859 (pt) cc_final: 0.8586 (mt) REVERT: B 1992 TYR cc_start: 0.8378 (t80) cc_final: 0.8018 (t80) REVERT: B 2104 TRP cc_start: 0.7902 (t-100) cc_final: 0.6847 (m-90) REVERT: B 2364 TYR cc_start: 0.8008 (m-10) cc_final: 0.7770 (m-10) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0613 time to fit residues: 10.7354 Evaluate side-chains 89 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [11, 54, 82, 28, 22, 60, 20, 91, 1, 37, 52] chunk 11 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 28 optimal weight: 0.0060 chunk 22 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 37 optimal weight: 0.0000 chunk 52 optimal weight: 0.6980 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1571 HIS ** B2127 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 = 0.4327 r_free = 0.4327 target = 0.144443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.116554 restraints weight = 40031.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.116819 restraints weight = 28294.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.118687 restraints weight = 19209.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.120223 restraints weight = 13219.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.120542 restraints weight = 11678.165| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3953 r_free = 0.3953 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3953 r_free = 0.3953 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7958 Z= 0.101 Angle : 0.610 7.504 10808 Z= 0.303 Chirality : 0.045 0.135 1287 Planarity : 0.004 0.052 1369 Dihedral : 4.556 20.317 1105 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.91 % Favored : 89.89 % Rotamer: Outliers : 0.26 % Allowed : 1.43 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.25 (0.26), residues: 1022 helix: -0.87 (0.36), residues: 222 sheet: -1.62 (0.42), residues: 147 loop : -1.75 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1707 TYR 0.025 0.001 TYR B1747 PHE 0.008 0.001 PHE B2083 TRP 0.021 0.002 TRP B1705 HIS 0.004 0.001 HIS B1928 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 7958) covalent geometry : angle 0.61018 / 0.30 (10808) hydrogen bonds : bond 0.02870 / 2.02 ( 205) hydrogen bonds : angle 5.26298 / 3.62 ( 546) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: B 1709 ILE cc_start: 0.7216 (mm) cc_final: 0.6976 (mm) REVERT: B 1959 LEU cc_start: 0.8491 (pp) cc_final: 0.7822 (tp) REVERT: B 1991 ILE cc_start: 0.8851 (pt) cc_final: 0.8572 (mt) REVERT: B 1992 TYR cc_start: 0.8081 (t80) cc_final: 0.7738 (t80) REVERT: B 2104 TRP cc_start: 0.7736 (t-100) cc_final: 0.6868 (m-90) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.0601 time to fit residues: 11.1512 Evaluate side-chains 91 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [60, 66, 75, 39, 51, 74, 81, 5, 29, 21, 104] chunk 60 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1929 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2149 ASN ** B2510 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 = 0.4252 r_free = 0.4252 target = 0.138993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.104264 restraints weight = 44332.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.106662 restraints weight = 23085.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.108272 restraints weight = 15831.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.108472 restraints weight = 13961.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.108852 restraints weight = 12373.503| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3765 r_free = 0.3765 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3765 r_free = 0.3765 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7958 Z= 0.191 Angle : 0.704 10.644 10808 Z= 0.355 Chirality : 0.046 0.176 1287 Planarity : 0.005 0.054 1369 Dihedral : 4.982 21.443 1105 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.09 % Favored : 88.71 % Rotamer: Outliers : 0.26 % Allowed : 1.17 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.40 (0.25), residues: 1022 helix: -0.90 (0.35), residues: 229 sheet: -1.70 (0.39), residues: 163 loop : -1.88 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1707 TYR 0.021 0.002 TYR B2018 PHE 0.011 0.001 PHE B1792 TRP 0.032 0.002 TRP B2426 HIS 0.006 0.001 HIS B2433 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 ( 7958) covalent geometry : angle 0.70372 / 0.35 (10808) hydrogen bonds : bond 0.03444 / 2.33 ( 205) hydrogen bonds : angle 5.61772 / 3.82 ( 546) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: B 1709 ILE cc_start: 0.7441 (mm) cc_final: 0.7229 (mm) REVERT: B 1959 LEU cc_start: 0.8765 (pp) cc_final: 0.8032 (tp) REVERT: B 1991 ILE cc_start: 0.8941 (pt) cc_final: 0.8547 (mt) REVERT: B 2104 TRP cc_start: 0.7917 (t-100) cc_final: 0.6971 (t-100) REVERT: B 2455 VAL cc_start: 0.8844 (t) cc_final: 0.8643 (t) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.0656 time to fit residues: 9.9148 Evaluate side-chains 87 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [32, 93, 83, 66, 23, 17, 6, 71, 37, 74, 16] chunk 32 optimal weight: 0.0870 chunk 93 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 23 optimal weight: 20.0000 chunk 17 optimal weight: 30.0000 chunk 6 optimal weight: 0.0070 chunk 71 optimal weight: 2.9990 chunk 37 optimal weight: 0.0170 chunk 74 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1571 HIS ** B2127 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 = 0.4320 r_free = 0.4320 target = 0.143891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.111046 restraints weight = 52754.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.113044 restraints weight = 28065.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.115261 restraints weight = 18692.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.115733 restraints weight = 14802.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.115795 restraints weight = 13277.499| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3879 r_free = 0.3879 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3880 r_free = 0.3880 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7958 Z= 0.100 Angle : 0.627 9.972 10808 Z= 0.309 Chirality : 0.045 0.186 1287 Planarity : 0.004 0.056 1369 Dihedral : 4.620 21.432 1105 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.72 % Favored : 90.09 % Rotamer: Outliers : 0.26 % Allowed : 0.78 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.26), residues: 1022 helix: -0.64 (0.37), residues: 215 sheet: -1.74 (0.40), residues: 160 loop : -1.78 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1707 TYR 0.023 0.001 TYR B1747 PHE 0.008 0.001 PHE B2129 TRP 0.022 0.002 TRP B1705 HIS 0.003 0.001 HIS B1676 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 ( 7958) covalent geometry : angle 0.62667 / 0.31 (10808) hydrogen bonds : bond 0.02875 / 2.04 ( 205) hydrogen bonds : angle 5.23416 / 3.59 ( 546) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1646 MET cc_start: 0.4996 (tpt) cc_final: 0.4757 (tpp) REVERT: B 1959 LEU cc_start: 0.8625 (pp) cc_final: 0.7926 (tp) REVERT: B 1991 ILE cc_start: 0.8889 (pt) cc_final: 0.8617 (mt) REVERT: B 1992 TYR cc_start: 0.8121 (t80) cc_final: 0.7736 (t80) REVERT: B 2104 TRP cc_start: 0.7610 (t-100) cc_final: 0.7261 (t-100) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.0613 time to fit residues: 11.0623 Evaluate side-chains 92 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [6, 7, 86, 104, 89, 2, 61, 69, 84, 45, 82] chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 chunk 2 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 84 optimal weight: 0.0570 chunk 45 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1571 HIS ** B2127 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 = 0.4306 r_free = 0.4306 target = 0.142737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.111032 restraints weight = 51300.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.112796 restraints weight = 26083.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.114921 restraints weight = 18768.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.115270 restraints weight = 14246.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.116054 restraints weight = 13096.136| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3881 r_free = 0.3881 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3881 r_free = 0.3881 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7958 Z= 0.107 Angle : 0.615 9.991 10808 Z= 0.303 Chirality : 0.045 0.163 1287 Planarity : 0.004 0.055 1369 Dihedral : 4.559 21.520 1105 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.50 % Favored : 89.30 % Rotamer: Outliers : 0.26 % Allowed : 0.26 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.21 (0.26), residues: 1022 helix: -0.61 (0.37), residues: 221 sheet: -1.68 (0.40), residues: 160 loop : -1.78 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B2045 TYR 0.014 0.001 TYR B1992 PHE 0.006 0.001 PHE B2129 TRP 0.021 0.002 TRP B1705 HIS 0.004 0.001 HIS B1676 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 7958) covalent geometry : angle 0.61505 / 0.30 (10808) hydrogen bonds : bond 0.02769 / 1.93 ( 205) hydrogen bonds : angle 5.18509 / 3.56 ( 546) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1959 LEU cc_start: 0.8651 (pp) cc_final: 0.7926 (tp) REVERT: B 1991 ILE cc_start: 0.8912 (pt) cc_final: 0.8684 (mt) REVERT: B 1992 TYR cc_start: 0.8206 (t80) cc_final: 0.7914 (t80) REVERT: B 2104 TRP cc_start: 0.7501 (t-100) cc_final: 0.7131 (t-100) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.0658 time to fit residues: 11.2371 Evaluate side-chains 90 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [69, 5, 27, 93, 34, 1, 10, 103, 82, 20, 104] chunk 69 optimal weight: 0.9980 chunk 5 optimal weight: 0.0030 chunk 27 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 1 optimal weight: 0.0000 chunk 10 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 20 optimal weight: 0.0170 chunk 104 optimal weight: 0.9990 overall best weight: 0.3832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.144562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.116291 restraints weight = 38540.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.117574 restraints weight = 25686.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.119246 restraints weight = 18544.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.120116 restraints weight = 13051.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.120781 restraints weight = 11833.086| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3959 r_free = 0.3959 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3958 r_free = 0.3958 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7958 Z= 0.097 Angle : 0.610 9.583 10808 Z= 0.300 Chirality : 0.045 0.156 1287 Planarity : 0.004 0.057 1369 Dihedral : 4.446 21.480 1105 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.21 % Favored : 89.60 % Rotamer: Outliers : 0.26 % Allowed : 0.26 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.26), residues: 1022 helix: -0.52 (0.37), residues: 221 sheet: -1.54 (0.42), residues: 154 loop : -1.74 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1707 TYR 0.020 0.001 TYR B1747 PHE 0.008 0.001 PHE B1641 TRP 0.020 0.002 TRP B1705 HIS 0.005 0.001 HIS B1571 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 ( 7958) covalent geometry : angle 0.61045 / 0.30 (10808) hydrogen bonds : bond 0.02705 / 1.92 ( 205) hydrogen bonds : angle 5.07579 / 3.49 ( 546) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1959 LEU cc_start: 0.8566 (pp) cc_final: 0.7858 (tp) REVERT: B 1992 TYR cc_start: 0.8083 (t80) cc_final: 0.7731 (t80) REVERT: B 2104 TRP cc_start: 0.7217 (t-100) cc_final: 0.6836 (t-100) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.0606 time to fit residues: 10.4373 Evaluate side-chains 91 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: [22, 103, 28, 3, 82, 75, 13, 4, 20, 54, 31] chunk 22 optimal weight: 0.0970 chunk 103 optimal weight: 0.3980 chunk 28 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1571 HIS ** B2127 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 = 0.4332 r_free = 0.4332 target = 0.144847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.116524 restraints weight = 40709.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.118308 restraints weight = 25273.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.119880 restraints weight = 18529.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.120493 restraints weight = 13230.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.121398 restraints weight = 12214.832| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3968 r_free = 0.3968 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3968 r_free = 0.3968 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7958 Z= 0.097 Angle : 0.602 9.780 10808 Z= 0.297 Chirality : 0.044 0.153 1287 Planarity : 0.004 0.057 1369 Dihedral : 4.379 20.978 1105 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.79 % Favored : 89.01 % Rotamer: Outliers : 0.39 % Allowed : 0.00 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.26), residues: 1022 helix: -0.43 (0.37), residues: 227 sheet: -1.45 (0.41), residues: 162 loop : -1.78 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1707 TYR 0.017 0.001 TYR B1992 PHE 0.007 0.001 PHE B2129 TRP 0.020 0.002 TRP B1705 HIS 0.004 0.001 HIS B1571 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 ( 7958) covalent geometry : angle 0.60204 / 0.30 (10808) hydrogen bonds : bond 0.02664 / 1.88 ( 205) hydrogen bonds : angle 5.04908 / 3.48 ( 546) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1478.95 seconds wall clock time: 26 minutes 9.82 seconds (1569.82 seconds total)