Starting phenix.real_space_refine on Thu Aug 6 01:46:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ki6_37252/08_2026/8ki6_37252.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ki6_37252/08_2026/8ki6_37252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ki6_37252/08_2026/8ki6_37252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ki6_37252/08_2026/8ki6_37252.map" model { file = "/net/cci-nas-00/data/ceres_data/8ki6_37252/08_2026/8ki6_37252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ki6_37252/08_2026/8ki6_37252.cif" } resolution = 3.4 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= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 8156 2.51 5 N 2098 2.21 5 O 2407 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12751 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 12717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1580, 12717 Classifications: {'peptide': 1580} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 44, 'TRANS': 1535} Chain breaks: 11 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'RBV%rna2p': 1, 'RBV%rna3p': 1} Classifications: {'undetermined': 2} Modifications used: {'rna2p': 1, 'rna3p': 1} Link IDs: {'rna3p': 1} Time building chain proxies: 2.50, per 1000 atoms: 0.20 Number of scatterers: 12751 At special positions: 0 Unit cell: (116.63, 125.19, 111.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2407 8.00 N 2098 7.00 C 8156 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: 0.88 Conformation dependent library (CDL) restraints added in 424.4 milliseconds 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3048 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 6 sheets defined 59.7% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 337 through 345 removed outlier: 3.936A pdb=" N ARG A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 363 Processing helix chain 'A' and resid 364 through 367 Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'A' and resid 397 through 414 removed outlier: 3.532A pdb=" N LEU A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 432 removed outlier: 4.006A pdb=" N LYS A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 455 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.810A pdb=" N GLU A 465 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 466 " --> pdb=" O LEU A 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 466' Processing helix chain 'A' and resid 491 through 501 Processing helix chain 'A' and resid 521 through 536 Processing helix chain 'A' and resid 591 through 606 Processing helix chain 'A' and resid 664 through 682 Processing helix chain 'A' and resid 690 through 700 removed outlier: 3.566A pdb=" N VAL A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 removed outlier: 4.034A pdb=" N CYS A 704 " --> pdb=" O ASN A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 729 Processing helix chain 'A' and resid 730 through 749 Processing helix chain 'A' and resid 797 through 804 Processing helix chain 'A' and resid 828 through 837 Processing helix chain 'A' and resid 837 through 853 Proline residue: A 843 - end of helix Processing helix chain 'A' and resid 853 through 863 Processing helix chain 'A' and resid 874 through 893 removed outlier: 3.627A pdb=" N THR A 893 " --> pdb=" O VAL A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 909 removed outlier: 3.786A pdb=" N MET A 900 " --> pdb=" O LYS A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 927 Processing helix chain 'A' and resid 937 through 954 Processing helix chain 'A' and resid 992 through 1005 removed outlier: 3.758A pdb=" N TYR A 996 " --> pdb=" O LEU A 992 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 997 " --> pdb=" O GLU A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1036 removed outlier: 3.649A pdb=" N VAL A1023 " --> pdb=" O SER A1019 " (cutoff:3.500A) Proline residue: A1024 - end of helix removed outlier: 3.987A pdb=" N PHE A1031 " --> pdb=" O TRP A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1075 Processing helix chain 'A' and resid 1077 through 1089 Processing helix chain 'A' and resid 1094 through 1098 Processing helix chain 'A' and resid 1114 through 1125 Processing helix chain 'A' and resid 1126 through 1130 removed outlier: 3.717A pdb=" N ILE A1130 " --> pdb=" O ILE A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1151 Processing helix chain 'A' and resid 1151 through 1163 removed outlier: 3.878A pdb=" N LEU A1155 " --> pdb=" O GLU A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1180 removed outlier: 3.917A pdb=" N GLY A1180 " --> pdb=" O ILE A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1195 Processing helix chain 'A' and resid 1197 through 1209 removed outlier: 3.966A pdb=" N VAL A1201 " --> pdb=" O HIS A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1235 removed outlier: 3.895A pdb=" N TYR A1228 " --> pdb=" O SER A1224 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP A1229 " --> pdb=" O GLU A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1248 removed outlier: 3.688A pdb=" N VAL A1245 " --> pdb=" O ASP A1241 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET A1246 " --> pdb=" O LEU A1242 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A1248 " --> pdb=" O SER A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1271 Processing helix chain 'A' and resid 1300 through 1319 removed outlier: 4.830A pdb=" N HIS A1316 " --> pdb=" O HIS A1312 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL A1317 " --> pdb=" O THR A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1353 removed outlier: 4.344A pdb=" N ILE A1334 " --> pdb=" O GLY A1330 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG A1335 " --> pdb=" O ASP A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1386 removed outlier: 4.185A pdb=" N LEU A1382 " --> pdb=" O TYR A1378 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A1383 " --> pdb=" O LYS A1379 " (cutoff:3.500A) Processing helix chain 'A' and resid 1393 through 1408 Processing helix chain 'A' and resid 1414 through 1428 Processing helix chain 'A' and resid 1434 through 1439 Processing helix chain 'A' and resid 1459 through 1478 removed outlier: 3.719A pdb=" N SER A1463 " --> pdb=" O ASN A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1514 Processing helix chain 'A' and resid 1517 through 1533 Processing helix chain 'A' and resid 1565 through 1575 removed outlier: 3.693A pdb=" N CYS A1573 " --> pdb=" O LEU A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1598 removed outlier: 3.610A pdb=" N HIS A1591 " --> pdb=" O SER A1587 " (cutoff:3.500A) Processing helix chain 'A' and resid 1601 through 1603 No H-bonds generated for 'chain 'A' and resid 1601 through 1603' Processing helix chain 'A' and resid 1604 through 1620 Processing helix chain 'A' and resid 1630 through 1638 Processing helix chain 'A' and resid 1647 through 1651 Processing helix chain 'A' and resid 1657 through 1664 Processing helix chain 'A' and resid 1667 through 1682 Processing helix chain 'A' and resid 1686 through 1696 removed outlier: 3.624A pdb=" N SER A1696 " --> pdb=" O ASP A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1714 Processing helix chain 'A' and resid 1717 through 1733 Processing helix chain 'A' and resid 1762 through 1769 removed outlier: 3.827A pdb=" N ASN A1765 " --> pdb=" O ILE A1762 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A1767 " --> pdb=" O GLU A1764 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASN A1768 " --> pdb=" O ASN A1765 " (cutoff:3.500A) Processing helix chain 'A' and resid 1770 through 1777 Processing helix chain 'A' and resid 1814 through 1828 Processing helix chain 'A' and resid 1829 through 1835 removed outlier: 4.209A pdb=" N ILE A1833 " --> pdb=" O ASN A1829 " (cutoff:3.500A) Processing helix chain 'A' and resid 1843 through 1850 Processing helix chain 'A' and resid 1891 through 1904 Processing helix chain 'A' and resid 1910 through 1923 Processing helix chain 'A' and resid 1924 through 1936 Proline residue: A1932 - end of helix Processing helix chain 'A' and resid 1958 through 1965 Processing helix chain 'A' and resid 1986 through 2008 Processing helix chain 'A' and resid 2018 through 2030 removed outlier: 4.051A pdb=" N ASN A2030 " --> pdb=" O PHE A2026 " (cutoff:3.500A) Processing helix chain 'A' and resid 2031 through 2043 removed outlier: 4.232A pdb=" N MET A2042 " --> pdb=" O ALA A2038 " (cutoff:3.500A) Processing helix chain 'A' and resid 2052 through 2058 removed outlier: 3.770A pdb=" N ARG A2058 " --> pdb=" O THR A2054 " (cutoff:3.500A) Processing helix chain 'A' and resid 2059 through 2065 removed outlier: 3.680A pdb=" N PHE A2063 " --> pdb=" O LYS A2059 " (cutoff:3.500A) Processing helix chain 'A' and resid 2066 through 2069 Processing sheet with id=AA1, first strand: chain 'A' and resid 508 through 509 removed outlier: 3.682A pdb=" N TYR A 811 " --> pdb=" O ILE A 508 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 810 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 508 through 509 removed outlier: 3.682A pdb=" N TYR A 811 " --> pdb=" O ILE A 508 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 810 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1483 through 1492 removed outlier: 3.899A pdb=" N HIS A1492 " --> pdb=" O ASP A1495 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1411 through 1412 Processing sheet with id=AA5, first strand: chain 'A' and resid 1548 through 1549 Processing sheet with id=AA6, first strand: chain 'A' and resid 1973 through 1975 removed outlier: 3.868A pdb=" N ILE A2084 " --> pdb=" O VAL A1974 " (cutoff:3.500A) 671 hydrogen bonds defined for protein. 1944 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: 2.53 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2096 1.30 - 1.43: 3284 1.43 - 1.56: 7455 1.56 - 1.70: 6 1.70 - 1.83: 147 Bond restraints: 12988 Sorted by residual: bond pdb=" CA PRO A1960 " pdb=" CB PRO A1960 " ideal model delta sigma weight residual 1.533 1.441 0.092 1.42e-02 4.96e+03 4.18e+01 bond pdb=" C VAL A1962 " pdb=" O VAL A1962 " ideal model delta sigma weight residual 1.240 1.168 0.071 1.18e-02 7.18e+03 3.64e+01 bond pdb=" CA PRO A1960 " pdb=" C PRO A1960 " ideal model delta sigma weight residual 1.520 1.448 0.072 1.42e-02 4.96e+03 2.54e+01 bond pdb=" C TRP A1958 " pdb=" O TRP A1958 " ideal model delta sigma weight residual 1.232 1.185 0.048 1.38e-02 5.25e+03 1.19e+01 bond pdb=" CA SER A1965 " pdb=" CB SER A1965 " ideal model delta sigma weight residual 1.530 1.475 0.054 1.58e-02 4.01e+03 1.19e+01 ... (remaining 12983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.44: 17386 5.44 - 10.87: 98 10.87 - 16.31: 13 16.31 - 21.74: 1 21.74 - 27.18: 1 Bond angle restraints: 17499 Sorted by residual: angle pdb=" N PRO A1966 " pdb=" CA PRO A1966 " pdb=" CB PRO A1966 " ideal model delta sigma weight residual 103.25 87.83 15.42 1.05e+00 9.07e-01 2.16e+02 angle pdb=" N PRO A1966 " pdb=" CA PRO A1966 " pdb=" C PRO A1966 " ideal model delta sigma weight residual 112.47 139.65 -27.18 2.06e+00 2.36e-01 1.74e+02 angle pdb=" O LYS A1957 " pdb=" C LYS A1957 " pdb=" N TRP A1958 " ideal model delta sigma weight residual 122.59 135.61 -13.02 1.33e+00 5.65e-01 9.58e+01 angle pdb=" CA LYS A1957 " pdb=" C LYS A1957 " pdb=" N TRP A1958 " ideal model delta sigma weight residual 116.84 100.51 16.33 1.71e+00 3.42e-01 9.12e+01 angle pdb=" N PRO A1960 " pdb=" CA PRO A1960 " pdb=" C PRO A1960 " ideal model delta sigma weight residual 112.47 98.20 14.27 2.06e+00 2.36e-01 4.80e+01 ... (remaining 17494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 6823 17.58 - 35.15: 891 35.15 - 52.73: 201 52.73 - 70.30: 35 70.30 - 87.88: 19 Dihedral angle restraints: 7969 sinusoidal: 3284 harmonic: 4685 Sorted by residual: dihedral pdb=" C TRP A1958 " pdb=" N TRP A1958 " pdb=" CA TRP A1958 " pdb=" CB TRP A1958 " ideal model delta harmonic sigma weight residual -122.60 -106.72 -15.88 0 2.50e+00 1.60e-01 4.03e+01 dihedral pdb=" N TRP A1958 " pdb=" C TRP A1958 " pdb=" CA TRP A1958 " pdb=" CB TRP A1958 " ideal model delta harmonic sigma weight residual 122.80 108.09 14.71 0 2.50e+00 1.60e-01 3.46e+01 dihedral pdb=" CA TYR A2085 " pdb=" C TYR A2085 " pdb=" N SER A2086 " pdb=" CA SER A2086 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 7966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1935 0.131 - 0.261: 52 0.261 - 0.392: 3 0.392 - 0.522: 0 0.522 - 0.653: 1 Chirality restraints: 1991 Sorted by residual: chirality pdb=" CA PRO A1966 " pdb=" N PRO A1966 " pdb=" C PRO A1966 " pdb=" CB PRO A1966 " both_signs ideal model delta sigma weight residual False 2.72 2.07 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CG LEU A 912 " pdb=" CB LEU A 912 " pdb=" CD1 LEU A 912 " pdb=" CD2 LEU A 912 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CG LEU A 677 " pdb=" CB LEU A 677 " pdb=" CD1 LEU A 677 " pdb=" CD2 LEU A 677 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 1988 not shown) Planarity restraints: 2186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A1957 " 0.023 2.00e-02 2.50e+03 5.63e-02 3.17e+01 pdb=" C LYS A1957 " -0.097 2.00e-02 2.50e+03 pdb=" O LYS A1957 " 0.041 2.00e-02 2.50e+03 pdb=" N TRP A1958 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A1958 " 0.025 2.00e-02 2.50e+03 5.04e-02 2.54e+01 pdb=" C TRP A1958 " -0.087 2.00e-02 2.50e+03 pdb=" O TRP A1958 " 0.032 2.00e-02 2.50e+03 pdb=" N ILE A1959 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1952 " -0.019 2.00e-02 2.50e+03 2.65e-02 1.75e+01 pdb=" CG TRP A1952 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP A1952 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP A1952 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A1952 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1952 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1952 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1952 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1952 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A1952 " 0.003 2.00e-02 2.50e+03 ... (remaining 2183 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2210 2.77 - 3.30: 11807 3.30 - 3.84: 20431 3.84 - 4.37: 22637 4.37 - 4.90: 40263 Nonbonded interactions: 97348 Sorted by model distance: nonbonded pdb=" O LYS A1440 " pdb=" OG1 THR A1443 " model vdw 2.238 3.040 nonbonded pdb=" O VAL A1997 " pdb=" OG1 THR A2001 " model vdw 2.267 3.040 nonbonded pdb=" O PRO A 512 " pdb=" OG1 THR A 805 " model vdw 2.296 3.040 nonbonded pdb=" OG SER A1372 " pdb=" O TRP A1453 " model vdw 2.299 3.040 nonbonded pdb=" OG SER A1372 " pdb=" OD1 ASN A1452 " model vdw 2.305 3.040 ... (remaining 97343 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.750 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 12988 Z= 0.268 Angle : 1.093 27.178 17499 Z= 0.597 Chirality : 0.055 0.653 1991 Planarity : 0.006 0.063 2186 Dihedral : 16.708 87.881 4921 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.13 % Favored : 92.54 % Rotamer: Outliers : 2.06 % Allowed : 16.59 % Favored : 81.35 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % 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: -1.93 (0.19), residues: 1556 helix: -0.59 (0.15), residues: 876 sheet: 0.58 (0.66), residues: 62 loop : -2.46 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A2034 TYR 0.058 0.002 TYR A2085 PHE 0.046 0.002 PHE A1950 TRP 0.070 0.003 TRP A1952 HIS 0.023 0.001 HIS A1823 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.27 (12988) covalent geometry : angle 1.09313 / 0.60 (17499) hydrogen bonds : bond 0.07816 / 5.10 ( 661) hydrogen bonds : angle 5.25461 / 3.67 ( 1944) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 440 ILE cc_start: 0.7461 (tt) cc_final: 0.7147 (mt) REVERT: A 822 MET cc_start: 0.8299 (mmm) cc_final: 0.8021 (mmt) REVERT: A 926 ASP cc_start: 0.7214 (t0) cc_final: 0.6962 (m-30) REVERT: A 1034 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7403 (tm-30) REVERT: A 1757 LYS cc_start: 0.5831 (tttm) cc_final: 0.5620 (tttm) outliers start: 30 outliers final: 22 residues processed: 220 average time/residue: 0.0925 time to fit residues: 30.7330 Evaluate side-chains 206 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 1019 SER Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1247 ASN Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1613 GLN Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 2071 ARG Chi-restraints excluded: chain A residue 2076 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN A1213 ASN A1578 HIS ** A2040 ASN ** 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 = 0.4204 r_free = 0.4204 target = 0.176464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.141444 restraints weight = 18080.602| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.74 r_work: 0.3685 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12988 Z= 0.137 Angle : 0.621 9.706 17499 Z= 0.324 Chirality : 0.043 0.193 1991 Planarity : 0.004 0.056 2186 Dihedral : 8.511 78.083 1770 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.30 % Favored : 93.51 % Rotamer: Outliers : 2.34 % Allowed : 16.59 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.21), residues: 1556 helix: 0.57 (0.17), residues: 889 sheet: 0.44 (0.69), residues: 62 loop : -2.32 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2034 TYR 0.017 0.001 TYR A2064 PHE 0.027 0.001 PHE A2061 TRP 0.032 0.002 TRP A1958 HIS 0.005 0.001 HIS A1235 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (12988) covalent geometry : angle 0.62054 / 0.32 (17499) hydrogen bonds : bond 0.04274 / 2.91 ( 661) hydrogen bonds : angle 4.26291 / 2.96 ( 1944) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 0.321 Fit side-chains REVERT: A 440 ILE cc_start: 0.7626 (tt) cc_final: 0.7142 (mt) REVERT: A 587 MET cc_start: 0.8570 (pmm) cc_final: 0.8368 (pmm) REVERT: A 1021 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7652 (tt) REVERT: A 1049 MET cc_start: 0.8305 (mmm) cc_final: 0.8069 (ttt) REVERT: A 1109 GLN cc_start: 0.8251 (pt0) cc_final: 0.7958 (pt0) REVERT: A 1246 MET cc_start: 0.7618 (mmm) cc_final: 0.7388 (mmp) REVERT: A 1635 LYS cc_start: 0.9097 (tttp) cc_final: 0.8830 (ttmt) REVERT: A 1819 MET cc_start: 0.6962 (tpt) cc_final: 0.6680 (tpt) REVERT: A 1823 HIS cc_start: 0.6610 (p-80) cc_final: 0.6184 (p-80) outliers start: 34 outliers final: 21 residues processed: 216 average time/residue: 0.0868 time to fit residues: 28.8663 Evaluate side-chains 196 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1594 MET Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1961 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 109 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 ASN A1602 ASN ** A1613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1978 ASN ** A2040 ASN ** 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 = 0.4168 r_free = 0.4168 target = 0.173075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.138212 restraints weight = 18693.991| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.07 r_work: 0.3645 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12988 Z= 0.156 Angle : 0.620 11.552 17499 Z= 0.325 Chirality : 0.043 0.184 1991 Planarity : 0.004 0.053 2186 Dihedral : 8.101 77.322 1746 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.75 % Favored : 93.12 % Rotamer: Outliers : 3.65 % Allowed : 17.62 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.22), residues: 1556 helix: 0.88 (0.18), residues: 892 sheet: 0.46 (0.69), residues: 61 loop : -2.28 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1705 TYR 0.016 0.002 TYR A1911 PHE 0.037 0.002 PHE A1950 TRP 0.022 0.002 TRP A1958 HIS 0.005 0.001 HIS A1492 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (12988) covalent geometry : angle 0.62038 / 0.33 (17499) hydrogen bonds : bond 0.04604 / 3.12 ( 661) hydrogen bonds : angle 4.22297 / 2.92 ( 1944) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 184 time to evaluate : 0.486 Fit side-chains REVERT: A 440 ILE cc_start: 0.7760 (tt) cc_final: 0.7395 (mt) REVERT: A 809 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.7650 (t80) REVERT: A 1021 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7452 (tt) REVERT: A 1555 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6833 (mtp85) REVERT: A 1819 MET cc_start: 0.6739 (tpt) cc_final: 0.6521 (tpt) REVERT: A 1823 HIS cc_start: 0.6740 (p-80) cc_final: 0.6275 (p-80) REVERT: A 1896 MET cc_start: 0.8469 (tpp) cc_final: 0.8197 (tpp) outliers start: 53 outliers final: 32 residues processed: 224 average time/residue: 0.0978 time to fit residues: 33.4910 Evaluate side-chains 210 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1272 ASN Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1471 LYS Chi-restraints excluded: chain A residue 1555 ARG Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 15 optimal weight: 1.9990 chunk 136 optimal weight: 0.4980 chunk 157 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 153 optimal weight: 0.4980 chunk 67 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN A1124 ASN ** A1613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.174730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.139658 restraints weight = 18183.063| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.73 r_work: 0.3660 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12988 Z= 0.118 Angle : 0.576 11.213 17499 Z= 0.300 Chirality : 0.041 0.170 1991 Planarity : 0.004 0.068 2186 Dihedral : 7.851 76.853 1744 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.30 % Favored : 93.57 % Rotamer: Outliers : 3.58 % Allowed : 18.17 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.22), residues: 1556 helix: 1.12 (0.18), residues: 891 sheet: 0.57 (0.70), residues: 61 loop : -2.21 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2034 TYR 0.014 0.001 TYR A2085 PHE 0.037 0.001 PHE A2061 TRP 0.021 0.001 TRP A1952 HIS 0.003 0.001 HIS A1492 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (12988) covalent geometry : angle 0.57588 / 0.30 (17499) hydrogen bonds : bond 0.03994 / 2.72 ( 661) hydrogen bonds : angle 4.07976 / 2.82 ( 1944) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 369 GLU cc_start: 0.7915 (pp20) cc_final: 0.7423 (pm20) REVERT: A 440 ILE cc_start: 0.7717 (tt) cc_final: 0.7362 (mt) REVERT: A 809 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.7502 (t80) REVERT: A 1021 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7400 (tt) REVERT: A 1109 GLN cc_start: 0.8137 (pt0) cc_final: 0.7838 (pt0) REVERT: A 1819 MET cc_start: 0.6676 (tpt) cc_final: 0.6204 (tpt) REVERT: A 1823 HIS cc_start: 0.6811 (OUTLIER) cc_final: 0.6438 (p-80) REVERT: A 1872 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7467 (ptp-170) REVERT: A 1896 MET cc_start: 0.8495 (tpp) cc_final: 0.8181 (tpp) REVERT: A 1954 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7358 (mm-40) REVERT: A 2006 LEU cc_start: 0.6734 (tp) cc_final: 0.6372 (tp) REVERT: A 2084 ILE cc_start: 0.6857 (tp) cc_final: 0.6432 (tp) outliers start: 52 outliers final: 32 residues processed: 221 average time/residue: 0.1028 time to fit residues: 34.2906 Evaluate side-chains 212 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1124 ASN Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1594 MET Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1823 HIS Chi-restraints excluded: chain A residue 1831 GLU Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1872 ARG Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 2071 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 146 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN A1011 HIS A1124 ASN ** A1613 GLN ** 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 = 0.4151 r_free = 0.4151 target = 0.171358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.135966 restraints weight = 18407.151| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.73 r_work: 0.3636 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12988 Z= 0.158 Angle : 0.614 13.829 17499 Z= 0.318 Chirality : 0.043 0.186 1991 Planarity : 0.004 0.072 2186 Dihedral : 7.820 76.824 1744 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.75 % Favored : 93.06 % Rotamer: Outliers : 4.20 % Allowed : 17.96 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.22), residues: 1556 helix: 1.11 (0.18), residues: 895 sheet: 0.39 (0.69), residues: 61 loop : -2.20 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2034 TYR 0.014 0.001 TYR A 804 PHE 0.038 0.002 PHE A1950 TRP 0.023 0.002 TRP A1952 HIS 0.006 0.001 HIS A1492 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (12988) covalent geometry : angle 0.61351 / 0.32 (17499) hydrogen bonds : bond 0.04502 / 3.06 ( 661) hydrogen bonds : angle 4.17087 / 2.88 ( 1944) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 180 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6060 (OUTLIER) cc_final: 0.5321 (m-10) REVERT: A 440 ILE cc_start: 0.7775 (tt) cc_final: 0.7456 (mt) REVERT: A 809 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.7569 (t80) REVERT: A 1021 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7449 (tt) REVERT: A 1109 GLN cc_start: 0.8204 (pt0) cc_final: 0.7914 (pt0) REVERT: A 1555 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6789 (mtp85) REVERT: A 1691 LYS cc_start: 0.7966 (ttpt) cc_final: 0.7208 (tptp) REVERT: A 1823 HIS cc_start: 0.6946 (OUTLIER) cc_final: 0.6570 (p-80) REVERT: A 1872 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7477 (ptp-170) REVERT: A 1896 MET cc_start: 0.8502 (tpp) cc_final: 0.8179 (tpp) REVERT: A 1954 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7373 (mm-40) REVERT: A 2006 LEU cc_start: 0.6835 (tp) cc_final: 0.6522 (tt) REVERT: A 2084 ILE cc_start: 0.7142 (tp) cc_final: 0.6727 (tp) outliers start: 61 outliers final: 41 residues processed: 230 average time/residue: 0.1026 time to fit residues: 35.3505 Evaluate side-chains 218 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1124 ASN Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1247 ASN Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1471 LYS Chi-restraints excluded: chain A residue 1555 ARG Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1823 HIS Chi-restraints excluded: chain A residue 1831 GLU Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1872 ARG Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 2014 LEU Chi-restraints excluded: chain A residue 2071 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 143 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN A1011 HIS A1124 ASN A1349 ASN ** A1613 GLN ** 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 = 0.4147 r_free = 0.4147 target = 0.170913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.135624 restraints weight = 18053.863| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.72 r_work: 0.3631 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12988 Z= 0.153 Angle : 0.619 14.650 17499 Z= 0.318 Chirality : 0.043 0.167 1991 Planarity : 0.004 0.070 2186 Dihedral : 7.749 76.661 1744 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.49 % Favored : 93.32 % Rotamer: Outliers : 4.13 % Allowed : 18.24 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.22), residues: 1556 helix: 1.14 (0.18), residues: 894 sheet: 0.37 (0.69), residues: 61 loop : -2.22 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2034 TYR 0.016 0.001 TYR A1465 PHE 0.037 0.002 PHE A2061 TRP 0.027 0.002 TRP A1952 HIS 0.010 0.001 HIS A1011 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (12988) covalent geometry : angle 0.61883 / 0.32 (17499) hydrogen bonds : bond 0.04484 / 3.05 ( 661) hydrogen bonds : angle 4.17295 / 2.88 ( 1944) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 171 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6178 (OUTLIER) cc_final: 0.5422 (m-10) REVERT: A 369 GLU cc_start: 0.7909 (pp20) cc_final: 0.7400 (pm20) REVERT: A 440 ILE cc_start: 0.7806 (tt) cc_final: 0.7487 (mt) REVERT: A 809 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.7546 (t80) REVERT: A 1006 MET cc_start: 0.8830 (mmm) cc_final: 0.8351 (mmm) REVERT: A 1021 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7411 (tt) REVERT: A 1109 GLN cc_start: 0.8219 (pt0) cc_final: 0.7948 (pt0) REVERT: A 1555 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6825 (mtp85) REVERT: A 1691 LYS cc_start: 0.7971 (ttpt) cc_final: 0.7174 (tttp) REVERT: A 1823 HIS cc_start: 0.6918 (OUTLIER) cc_final: 0.6520 (p-80) REVERT: A 2006 LEU cc_start: 0.7037 (tp) cc_final: 0.6743 (tt) REVERT: A 2084 ILE cc_start: 0.7169 (tp) cc_final: 0.6787 (tp) outliers start: 60 outliers final: 45 residues processed: 221 average time/residue: 0.0795 time to fit residues: 26.4985 Evaluate side-chains 216 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 166 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1124 ASN Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1247 ASN Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1471 LYS Chi-restraints excluded: chain A residue 1555 ARG Chi-restraints excluded: chain A residue 1594 MET Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1823 HIS Chi-restraints excluded: chain A residue 1831 GLU Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1872 ARG Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 2014 LEU Chi-restraints excluded: chain A residue 2071 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 85 optimal weight: 0.0980 chunk 157 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 113 optimal weight: 0.0050 chunk 2 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1954 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 = 0.4176 r_free = 0.4176 target = 0.173575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.138506 restraints weight = 18023.974| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.70 r_work: 0.3665 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12988 Z= 0.119 Angle : 0.587 13.043 17499 Z= 0.303 Chirality : 0.041 0.217 1991 Planarity : 0.004 0.064 2186 Dihedral : 7.529 76.507 1744 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.98 % Favored : 93.83 % Rotamer: Outliers : 3.44 % Allowed : 18.79 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.22), residues: 1556 helix: 1.25 (0.18), residues: 896 sheet: 0.54 (0.69), residues: 61 loop : -2.16 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2034 TYR 0.014 0.001 TYR A 923 PHE 0.036 0.001 PHE A1950 TRP 0.029 0.001 TRP A1952 HIS 0.016 0.001 HIS A1011 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (12988) covalent geometry : angle 0.58736 / 0.30 (17499) hydrogen bonds : bond 0.03997 / 2.72 ( 661) hydrogen bonds : angle 4.05862 / 2.80 ( 1944) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 177 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6099 (OUTLIER) cc_final: 0.5313 (m-10) REVERT: A 369 GLU cc_start: 0.7878 (pp20) cc_final: 0.7380 (pm20) REVERT: A 440 ILE cc_start: 0.7753 (tt) cc_final: 0.7426 (mt) REVERT: A 809 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.7615 (t80) REVERT: A 1006 MET cc_start: 0.8799 (mmm) cc_final: 0.8330 (mmm) REVERT: A 1021 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7429 (tt) REVERT: A 1109 GLN cc_start: 0.8206 (pt0) cc_final: 0.7970 (pt0) REVERT: A 1555 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.7058 (mtt90) REVERT: A 1691 LYS cc_start: 0.8031 (ttpt) cc_final: 0.7247 (tptp) REVERT: A 1823 HIS cc_start: 0.6842 (OUTLIER) cc_final: 0.6436 (p-80) REVERT: A 2006 LEU cc_start: 0.6979 (tp) cc_final: 0.6714 (tt) REVERT: A 2084 ILE cc_start: 0.6930 (tp) cc_final: 0.6545 (tp) outliers start: 50 outliers final: 42 residues processed: 217 average time/residue: 0.0806 time to fit residues: 26.6448 Evaluate side-chains 214 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 167 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1247 ASN Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1555 ARG Chi-restraints excluded: chain A residue 1594 MET Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1628 ASN Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1823 HIS Chi-restraints excluded: chain A residue 1831 GLU Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 2014 LEU Chi-restraints excluded: chain A residue 2071 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 1 optimal weight: 0.0980 chunk 105 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 119 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 HIS A1124 ASN ** A1613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.178431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.145320 restraints weight = 17773.055| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.66 r_work: 0.3681 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12988 Z= 0.113 Angle : 0.576 12.410 17499 Z= 0.297 Chirality : 0.041 0.178 1991 Planarity : 0.004 0.059 2186 Dihedral : 7.259 76.498 1742 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.17 % Favored : 93.64 % Rotamer: Outliers : 3.23 % Allowed : 19.20 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.22), residues: 1556 helix: 1.36 (0.18), residues: 899 sheet: 0.61 (0.71), residues: 61 loop : -2.11 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2034 TYR 0.015 0.001 TYR A 923 PHE 0.036 0.001 PHE A1950 TRP 0.035 0.001 TRP A1952 HIS 0.002 0.001 HIS A1235 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (12988) covalent geometry : angle 0.57553 / 0.30 (17499) hydrogen bonds : bond 0.03727 / 2.53 ( 661) hydrogen bonds : angle 3.95212 / 2.72 ( 1944) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 440 ILE cc_start: 0.7655 (tt) cc_final: 0.7324 (mt) REVERT: A 809 TYR cc_start: 0.7897 (OUTLIER) cc_final: 0.7695 (t80) REVERT: A 1006 MET cc_start: 0.8750 (mmm) cc_final: 0.8309 (mmm) REVERT: A 1109 GLN cc_start: 0.8108 (pt0) cc_final: 0.7872 (pt0) REVERT: A 1555 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6977 (mtt90) REVERT: A 1823 HIS cc_start: 0.6731 (OUTLIER) cc_final: 0.6410 (p-80) outliers start: 47 outliers final: 39 residues processed: 214 average time/residue: 0.0974 time to fit residues: 31.4926 Evaluate side-chains 207 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1124 ASN Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1555 ARG Chi-restraints excluded: chain A residue 1594 MET Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1628 ASN Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1823 HIS Chi-restraints excluded: chain A residue 1831 GLU Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 2014 LEU Chi-restraints excluded: chain A residue 2071 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 8 optimal weight: 0.0770 chunk 25 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 44 optimal weight: 0.3980 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 HIS A1124 ASN ** A1613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.177368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.143754 restraints weight = 18079.407| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.70 r_work: 0.3653 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12988 Z= 0.136 Angle : 0.605 13.275 17499 Z= 0.310 Chirality : 0.042 0.184 1991 Planarity : 0.004 0.059 2186 Dihedral : 7.184 76.508 1740 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.30 % Favored : 93.51 % Rotamer: Outliers : 3.37 % Allowed : 19.27 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.22), residues: 1556 helix: 1.32 (0.18), residues: 899 sheet: 0.50 (0.70), residues: 62 loop : -2.11 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2034 TYR 0.012 0.001 TYR A2064 PHE 0.037 0.001 PHE A1950 TRP 0.044 0.002 TRP A1952 HIS 0.004 0.001 HIS A1492 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (12988) covalent geometry : angle 0.60502 / 0.31 (17499) hydrogen bonds : bond 0.04046 / 2.74 ( 661) hydrogen bonds : angle 4.01645 / 2.77 ( 1944) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6143 (OUTLIER) cc_final: 0.5358 (m-10) REVERT: A 369 GLU cc_start: 0.7881 (pp20) cc_final: 0.7357 (pm20) REVERT: A 440 ILE cc_start: 0.7708 (tt) cc_final: 0.7374 (mt) REVERT: A 809 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.7724 (t80) REVERT: A 1006 MET cc_start: 0.8774 (mmm) cc_final: 0.8295 (mmm) REVERT: A 1109 GLN cc_start: 0.8168 (pt0) cc_final: 0.7944 (pt0) REVERT: A 1555 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.7038 (mtt90) REVERT: A 1713 LYS cc_start: 0.7662 (mttp) cc_final: 0.7239 (ttmm) REVERT: A 1823 HIS cc_start: 0.6798 (OUTLIER) cc_final: 0.6423 (p-80) REVERT: A 1971 MET cc_start: 0.6432 (tpp) cc_final: 0.6022 (tpp) REVERT: A 2006 LEU cc_start: 0.6810 (tt) cc_final: 0.6427 (tp) REVERT: A 2034 ARG cc_start: 0.7084 (mmm-85) cc_final: 0.6815 (mmm-85) REVERT: A 2084 ILE cc_start: 0.6840 (tp) cc_final: 0.6503 (tp) outliers start: 49 outliers final: 39 residues processed: 209 average time/residue: 0.1003 time to fit residues: 31.6069 Evaluate side-chains 210 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 167 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 803 CYS Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1124 ASN Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1247 ASN Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1555 ARG Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1823 HIS Chi-restraints excluded: chain A residue 1831 GLU Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 2014 LEU Chi-restraints excluded: chain A residue 2071 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 152 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 HIS A1124 ASN ** A1613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.171099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.138338 restraints weight = 18307.925| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.72 r_work: 0.3599 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12988 Z= 0.204 Angle : 0.689 16.678 17499 Z= 0.352 Chirality : 0.045 0.184 1991 Planarity : 0.004 0.065 2186 Dihedral : 7.415 76.415 1740 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.94 % Favored : 92.87 % Rotamer: Outliers : 3.23 % Allowed : 19.41 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.22), residues: 1556 helix: 1.11 (0.18), residues: 894 sheet: 0.27 (0.70), residues: 62 loop : -2.23 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2034 TYR 0.016 0.002 TYR A 804 PHE 0.029 0.002 PHE A 478 TRP 0.051 0.002 TRP A1952 HIS 0.012 0.002 HIS A1011 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.20 (12988) covalent geometry : angle 0.68942 / 0.35 (17499) hydrogen bonds : bond 0.04964 / 3.37 ( 661) hydrogen bonds : angle 4.26289 / 2.94 ( 1944) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 325 TYR cc_start: 0.6359 (OUTLIER) cc_final: 0.5464 (m-10) REVERT: A 369 GLU cc_start: 0.7928 (pp20) cc_final: 0.7379 (pm20) REVERT: A 440 ILE cc_start: 0.7766 (tt) cc_final: 0.7494 (mt) REVERT: A 809 TYR cc_start: 0.8005 (OUTLIER) cc_final: 0.7699 (t80) REVERT: A 1006 MET cc_start: 0.8771 (mmm) cc_final: 0.8287 (mmm) REVERT: A 1049 MET cc_start: 0.7945 (ttt) cc_final: 0.7706 (tpt) REVERT: A 1555 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.6832 (mtp85) REVERT: A 1713 LYS cc_start: 0.7714 (mttp) cc_final: 0.7319 (ttmm) REVERT: A 1823 HIS cc_start: 0.6848 (OUTLIER) cc_final: 0.6388 (p-80) REVERT: A 1872 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7773 (ptp-170) REVERT: A 1971 MET cc_start: 0.6421 (tpp) cc_final: 0.6096 (tpp) outliers start: 47 outliers final: 39 residues processed: 203 average time/residue: 0.0899 time to fit residues: 27.3191 Evaluate side-chains 208 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 896 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1124 ASN Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1217 VAL Chi-restraints excluded: chain A residue 1247 ASN Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1555 ARG Chi-restraints excluded: chain A residue 1619 ILE Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1823 HIS Chi-restraints excluded: chain A residue 1831 GLU Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1872 ARG Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 2014 LEU Chi-restraints excluded: chain A residue 2071 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 156 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 108 optimal weight: 0.5980 chunk 22 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 73 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1613 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 = 0.4146 r_free = 0.4146 target = 0.175116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.141222 restraints weight = 18104.144| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.65 r_work: 0.3619 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12988 Z= 0.150 Angle : 0.636 15.443 17499 Z= 0.325 Chirality : 0.043 0.184 1991 Planarity : 0.004 0.064 2186 Dihedral : 7.328 76.304 1740 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.11 % Favored : 93.70 % Rotamer: Outliers : 3.10 % Allowed : 19.82 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.22), residues: 1556 helix: 1.15 (0.18), residues: 899 sheet: 0.41 (0.71), residues: 62 loop : -2.21 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2034 TYR 0.014 0.001 TYR A 923 PHE 0.025 0.001 PHE A 478 TRP 0.045 0.002 TRP A1952 HIS 0.005 0.001 HIS A1492 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (12988) covalent geometry : angle 0.63644 / 0.33 (17499) hydrogen bonds : bond 0.04399 / 2.99 ( 661) hydrogen bonds : angle 4.14981 / 2.86 ( 1944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2396.50 seconds wall clock time: 42 minutes 6.49 seconds (2526.49 seconds total)