Starting phenix.real_space_refine on Thu Mar 5 07:45:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jge_22324/03_2026/7jge_22324.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jge_22324/03_2026/7jge_22324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jge_22324/03_2026/7jge_22324.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jge_22324/03_2026/7jge_22324.map" model { file = "/net/cci-nas-00/data/ceres_data/7jge_22324/03_2026/7jge_22324.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jge_22324/03_2026/7jge_22324.cif" } resolution = 4.0 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 86 5.16 5 C 7433 2.51 5 N 2012 2.21 5 O 2276 1.98 5 H 8508 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 116 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20315 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 20315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1437, 20315 Classifications: {'peptide': 1437} Link IDs: {'PTRANS': 38, 'TRANS': 1398} Chain breaks: 27 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 3.48, per 1000 atoms: 0.17 Number of scatterers: 20315 At special positions: 0 Unit cell: (115.322, 133.308, 136.482, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 O 2276 8.00 N 2012 7.00 C 7433 6.00 H 8508 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 228 " distance=2.03 Simple disulfide: pdb=" SG CYS A 67 " - pdb=" SG CYS A 106 " distance=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS A 645 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A 771 " - pdb=" SG CYS A 910 " distance=2.03 Simple disulfide: pdb=" SG CYS A 785 " - pdb=" SG CYS A 803 " distance=2.03 Simple disulfide: pdb=" SG CYS A 799 " - pdb=" SG CYS A 966 " distance=2.03 Simple disulfide: pdb=" SG CYS A 807 " - pdb=" SG CYS A 964 " distance=2.03 Simple disulfide: pdb=" SG CYS A 817 " - pdb=" SG CYS A 929 " distance=2.03 Simple disulfide: pdb=" SG CYS A 975 " - pdb=" SG CYS A1099 " distance=2.03 Simple disulfide: pdb=" SG CYS A 987 " - pdb=" SG CYS A1005 " distance=2.03 Simple disulfide: pdb=" SG CYS A1097 " - pdb=" SG CYS A1202 " distance=2.03 Simple disulfide: pdb=" SG CYS A1149 " - pdb=" SG CYS A1180 " distance=2.03 Simple disulfide: pdb=" SG CYS A1219 " - pdb=" SG CYS A1418 " distance=2.03 Simple disulfide: pdb=" SG CYS A1230 " - pdb=" SG CYS A1273 " distance=2.03 Simple disulfide: pdb=" SG CYS A1251 " - pdb=" SG CYS A1264 " distance=2.03 Simple disulfide: pdb=" SG CYS A1344 " - pdb=" SG CYS A1437 " distance=2.03 Simple disulfide: pdb=" SG CYS A1462 " - pdb=" SG CYS A1546 " distance=2.03 Simple disulfide: pdb=" SG CYS A1476 " - pdb=" SG CYS A1501 " distance=2.03 Simple disulfide: pdb=" SG CYS A1505 " - pdb=" SG CYS A1574 " distance=2.03 Simple disulfide: pdb=" SG CYS A1596 " - pdb=" SG CYS A1632 " distance=2.03 Simple disulfide: pdb=" SG CYS A1688 " - pdb=" SG CYS A1782 " distance=2.03 Simple disulfide: pdb=" SG CYS A1689 " - pdb=" SG CYS A1906 " distance=2.03 Simple disulfide: pdb=" SG CYS A1807 " - pdb=" SG CYS A1909 " distance=2.03 Simple disulfide: pdb=" SG CYS A1821 " - pdb=" SG CYS A1838 " distance=2.03 Simple disulfide: pdb=" SG CYS A1842 " - pdb=" SG CYS A1933 " distance=2.03 Simple disulfide: pdb=" SG CYS A1896 " - pdb=" SG CYS A1907 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 556.3 milliseconds 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2720 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 1 sheets defined 59.2% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 99 through 105 removed outlier: 4.084A pdb=" N ARG A 102 " --> pdb=" O PRO A 99 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 105 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 143 removed outlier: 3.997A pdb=" N PHE A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 166 removed outlier: 3.664A pdb=" N ILE A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 191 removed outlier: 3.586A pdb=" N GLU A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 222 Processing helix chain 'A' and resid 223 through 229 removed outlier: 4.633A pdb=" N ILE A 226 " --> pdb=" O TRP A 223 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N THR A 227 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY A 229 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 305 removed outlier: 3.610A pdb=" N GLU A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 355 removed outlier: 3.580A pdb=" N LYS A 355 " --> pdb=" O TYR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.654A pdb=" N GLN A 585 " --> pdb=" O PRO A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 591 Processing helix chain 'A' and resid 617 through 636 removed outlier: 4.422A pdb=" N SER A 621 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Proline residue: A 633 - end of helix Processing helix chain 'A' and resid 642 through 661 removed outlier: 4.213A pdb=" N LYS A 646 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 647 " --> pdb=" O ASN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 686 removed outlier: 3.962A pdb=" N LEU A 675 " --> pdb=" O LYS A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 722 removed outlier: 3.575A pdb=" N LEU A 707 " --> pdb=" O SER A 703 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LYS A 717 " --> pdb=" O ASN A 713 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N TYR A 718 " --> pdb=" O THR A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 785 removed outlier: 3.518A pdb=" N GLN A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP A 780 " --> pdb=" O ALA A 776 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 784 " --> pdb=" O ASP A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 815 Processing helix chain 'A' and resid 830 through 852 removed outlier: 3.663A pdb=" N ARG A 834 " --> pdb=" O PRO A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 893 Processing helix chain 'A' and resid 896 through 905 removed outlier: 3.526A pdb=" N TYR A 900 " --> pdb=" O THR A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 977 Processing helix chain 'A' and resid 1028 through 1052 removed outlier: 3.762A pdb=" N LYS A1040 " --> pdb=" O GLU A1036 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN A1043 " --> pdb=" O ASN A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1128 removed outlier: 3.729A pdb=" N ASP A1128 " --> pdb=" O LYS A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1158 removed outlier: 3.771A pdb=" N LYS A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR A1157 " --> pdb=" O TYR A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1180 removed outlier: 3.511A pdb=" N PHE A1175 " --> pdb=" O ASP A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1206 removed outlier: 3.876A pdb=" N CYS A1202 " --> pdb=" O ALA A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1271 removed outlier: 3.861A pdb=" N GLN A1270 " --> pdb=" O PRO A1266 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN A1271 " --> pdb=" O PRO A1267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1266 through 1271' Processing helix chain 'A' and resid 1296 through 1318 Processing helix chain 'A' and resid 1342 through 1360 removed outlier: 3.931A pdb=" N ALA A1346 " --> pdb=" O GLY A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1380 Processing helix chain 'A' and resid 1403 through 1428 Processing helix chain 'A' and resid 1449 through 1476 Processing helix chain 'A' and resid 1500 through 1530 removed outlier: 3.799A pdb=" N LYS A1504 " --> pdb=" O ALA A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1534 through 1542 removed outlier: 4.103A pdb=" N LEU A1538 " --> pdb=" O SER A1534 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A1542 " --> pdb=" O LEU A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1550 through 1555 Processing helix chain 'A' and resid 1570 through 1575 Processing helix chain 'A' and resid 1626 through 1631 removed outlier: 3.808A pdb=" N LEU A1631 " --> pdb=" O ARG A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1643 removed outlier: 4.303A pdb=" N ILE A1639 " --> pdb=" O GLU A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1646 through 1674 removed outlier: 5.010A pdb=" N GLU A1652 " --> pdb=" O GLU A1648 " (cutoff:3.500A) Processing helix chain 'A' and resid 1675 through 1678 Processing helix chain 'A' and resid 1680 through 1704 Processing helix chain 'A' and resid 1710 through 1724 removed outlier: 4.158A pdb=" N TYR A1715 " --> pdb=" O GLU A1711 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1744 Processing helix chain 'A' and resid 1755 through 1773 Processing helix chain 'A' and resid 1793 through 1821 Processing helix chain 'A' and resid 1837 through 1866 Proline residue: A1851 - end of helix removed outlier: 3.919A pdb=" N ILE A1854 " --> pdb=" O ASN A1850 " (cutoff:3.500A) Processing helix chain 'A' and resid 1887 through 1893 removed outlier: 3.511A pdb=" N LEU A1892 " --> pdb=" O VAL A1888 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A1893 " --> pdb=" O ILE A1889 " (cutoff:3.500A) Processing helix chain 'A' and resid 1915 through 1921 removed outlier: 3.974A pdb=" N THR A1921 " --> pdb=" O THR A1917 " (cutoff:3.500A) Processing helix chain 'A' and resid 1929 through 1949 removed outlier: 3.783A pdb=" N CYS A1933 " --> pdb=" O LYS A1929 " (cutoff:3.500A) Proline residue: A1939 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 920 through 923 609 hydrogen bonds defined for protein. 1800 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: 4.12 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 8495 1.04 - 1.23: 315 1.23 - 1.43: 4835 1.43 - 1.63: 6799 1.63 - 1.82: 103 Bond restraints: 20547 Sorted by residual: bond pdb=" CG PRO A1266 " pdb=" CD PRO A1266 " ideal model delta sigma weight residual 1.503 1.472 0.031 3.40e-02 8.65e+02 8.12e-01 bond pdb=" CG LEU A 294 " pdb=" CD2 LEU A 294 " ideal model delta sigma weight residual 1.521 1.549 -0.028 3.30e-02 9.18e+02 7.29e-01 bond pdb=" CB PRO A1266 " pdb=" CG PRO A1266 " ideal model delta sigma weight residual 1.492 1.534 -0.042 5.00e-02 4.00e+02 7.06e-01 bond pdb=" CG LEU A 294 " pdb=" CD1 LEU A 294 " ideal model delta sigma weight residual 1.521 1.548 -0.027 3.30e-02 9.18e+02 6.70e-01 bond pdb=" CA VAL A 266 " pdb=" C VAL A 266 " ideal model delta sigma weight residual 1.516 1.524 -0.009 1.11e-02 8.12e+03 5.92e-01 ... (remaining 20542 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.12: 35644 7.12 - 14.24: 2 14.24 - 21.36: 0 21.36 - 28.49: 6 28.49 - 35.61: 6 Bond angle restraints: 35658 Sorted by residual: angle pdb=" CB SER A 832 " pdb=" CA SER A 832 " pdb=" HA SER A 832 " ideal model delta sigma weight residual 109.00 73.39 35.61 3.00e+00 1.11e-01 1.41e+02 angle pdb=" N SER A 832 " pdb=" CA SER A 832 " pdb=" HA SER A 832 " ideal model delta sigma weight residual 110.00 75.90 34.10 3.00e+00 1.11e-01 1.29e+02 angle pdb=" C SER A 832 " pdb=" CA SER A 832 " pdb=" HA SER A 832 " ideal model delta sigma weight residual 109.00 74.99 34.01 3.00e+00 1.11e-01 1.29e+02 angle pdb=" SD MET A 186 " pdb=" CE MET A 186 " pdb=" HE2 MET A 186 " ideal model delta sigma weight residual 109.00 79.19 29.81 3.00e+00 1.11e-01 9.88e+01 angle pdb=" SD MET A 186 " pdb=" CE MET A 186 " pdb=" HE3 MET A 186 " ideal model delta sigma weight residual 109.00 79.25 29.75 3.00e+00 1.11e-01 9.83e+01 ... (remaining 35653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 9279 17.94 - 35.87: 625 35.87 - 53.81: 181 53.81 - 71.75: 31 71.75 - 89.68: 7 Dihedral angle restraints: 10123 sinusoidal: 5288 harmonic: 4835 Sorted by residual: dihedral pdb=" CB CYS A 799 " pdb=" SG CYS A 799 " pdb=" SG CYS A 966 " pdb=" CB CYS A 966 " ideal model delta sinusoidal sigma weight residual 93.00 42.49 50.51 1 1.00e+01 1.00e-02 3.49e+01 dihedral pdb=" CB CYS A 975 " pdb=" SG CYS A 975 " pdb=" SG CYS A1099 " pdb=" CB CYS A1099 " ideal model delta sinusoidal sigma weight residual 93.00 141.57 -48.57 1 1.00e+01 1.00e-02 3.25e+01 dihedral pdb=" CB CYS A1596 " pdb=" SG CYS A1596 " pdb=" SG CYS A1632 " pdb=" CB CYS A1632 " ideal model delta sinusoidal sigma weight residual 93.00 139.78 -46.78 1 1.00e+01 1.00e-02 3.03e+01 ... (remaining 10120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.343: 1665 0.343 - 0.687: 0 0.687 - 1.030: 0 1.030 - 1.373: 0 1.373 - 1.717: 1 Chirality restraints: 1666 Sorted by residual: chirality pdb=" CG LEU A 294 " pdb=" CB LEU A 294 " pdb=" CD1 LEU A 294 " pdb=" CD2 LEU A 294 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.37e+01 chirality pdb=" CA SER A 832 " pdb=" N SER A 832 " pdb=" C SER A 832 " pdb=" CB SER A 832 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA ILE A1250 " pdb=" N ILE A1250 " pdb=" C ILE A1250 " pdb=" CB ILE A1250 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 ... (remaining 1663 not shown) Planarity restraints: 3150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1265 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO A1266 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A1266 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1266 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 756 " 0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO A 757 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 757 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 757 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 665 " -0.008 2.00e-02 2.50e+03 5.31e-03 1.13e+00 pdb=" CG TRP A 665 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 665 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP A 665 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 665 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 665 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 665 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 665 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 665 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 665 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP A 665 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP A 665 " -0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP A 665 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 665 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 665 " -0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 665 " 0.000 2.00e-02 2.50e+03 ... (remaining 3147 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1351 2.23 - 2.83: 39301 2.83 - 3.42: 46456 3.42 - 4.01: 59943 4.01 - 4.60: 93714 Nonbonded interactions: 240765 Sorted by model distance: nonbonded pdb=" HE1 TRP A1761 " pdb=" O VAL A1785 " model vdw 1.643 2.450 nonbonded pdb="HH22 ARG A1628 " pdb=" OD2 ASP A1706 " model vdw 1.662 2.450 nonbonded pdb=" OE1 GLU A1652 " pdb=" H GLU A1652 " model vdw 1.665 2.450 nonbonded pdb=" OD1 ASP A 234 " pdb=" H LEU A 235 " model vdw 1.711 2.450 nonbonded pdb=" O ILE A1352 " pdb="HD21 ASN A1356 " model vdw 1.717 2.450 ... (remaining 240760 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.120 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.090 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5273 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 : 0.002 0.042 12066 Z= 0.092 Angle : 0.441 10.499 16221 Z= 0.257 Chirality : 0.053 1.717 1666 Planarity : 0.002 0.042 2068 Dihedral : 13.346 89.684 4569 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: 1.11 (0.24), residues: 1381 helix: 2.90 (0.19), residues: 775 sheet: 1.28 (2.16), residues: 10 loop : -2.48 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 851 TYR 0.009 0.001 TYR A 588 PHE 0.007 0.001 PHE A 652 TRP 0.018 0.001 TRP A 665 HIS 0.004 0.001 HIS A 845 Details of bonding type rmsd covalent geometry : bond 0.00181 (12039) covalent geometry : angle 0.43870 (16167) SS BOND : bond 0.00193 ( 27) SS BOND : angle 0.90807 ( 54) hydrogen bonds : bond 0.10911 ( 609) hydrogen bonds : angle 3.73945 ( 1800) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1731 ASP cc_start: 0.6645 (p0) cc_final: 0.5967 (p0) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1674 time to fit residues: 31.7170 Evaluate side-chains 110 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 591 ASN A 676 ASN ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN A 955 ASN A1037 GLN A1048 GLN A1368 HIS A1424 ASN A1522 GLN A1586 ASN A1794 GLN A1857 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.276825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.267633 restraints weight = 38480.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.263214 restraints weight = 44836.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.260237 restraints weight = 52287.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.260659 restraints weight = 48780.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.260820 restraints weight = 32263.495| |-----------------------------------------------------------------------------| r_work (final): 0.4549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5678 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12066 Z= 0.201 Angle : 0.560 10.441 16221 Z= 0.310 Chirality : 0.057 1.708 1666 Planarity : 0.004 0.040 2068 Dihedral : 3.346 23.011 1545 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.69 % Allowed : 7.13 % Favored : 92.18 % 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: 0.40 (0.23), residues: 1381 helix: 2.13 (0.18), residues: 812 sheet: None (None), residues: 0 loop : -2.74 (0.23), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 631 TYR 0.022 0.002 TYR A1867 PHE 0.024 0.002 PHE A 652 TRP 0.028 0.002 TRP A 560 HIS 0.004 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00457 (12039) covalent geometry : angle 0.55706 (16167) SS BOND : bond 0.00399 ( 27) SS BOND : angle 1.13403 ( 54) hydrogen bonds : bond 0.03776 ( 609) hydrogen bonds : angle 3.71411 ( 1800) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 836 ASP cc_start: 0.8233 (t70) cc_final: 0.7814 (t0) REVERT: A 844 LYS cc_start: 0.7096 (tttm) cc_final: 0.6748 (tptt) REVERT: A 1731 ASP cc_start: 0.7139 (p0) cc_final: 0.6413 (p0) REVERT: A 1935 GLU cc_start: 0.6502 (tp30) cc_final: 0.6161 (tm-30) outliers start: 9 outliers final: 7 residues processed: 140 average time/residue: 0.1951 time to fit residues: 40.0953 Evaluate side-chains 133 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 591 ASN Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 784 ASN Chi-restraints excluded: chain A residue 813 PHE Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1643 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 7 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.276872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.267083 restraints weight = 38603.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.261824 restraints weight = 47332.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.258736 restraints weight = 63882.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.258267 restraints weight = 52198.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.257158 restraints weight = 42343.520| |-----------------------------------------------------------------------------| r_work (final): 0.4618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5739 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12066 Z= 0.126 Angle : 0.463 10.365 16221 Z= 0.251 Chirality : 0.055 1.718 1666 Planarity : 0.003 0.036 2068 Dihedral : 3.242 20.028 1545 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.77 % Allowed : 9.28 % Favored : 89.95 % 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: 0.51 (0.23), residues: 1381 helix: 2.23 (0.19), residues: 811 sheet: None (None), residues: 0 loop : -2.71 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1895 TYR 0.013 0.001 TYR A1867 PHE 0.018 0.001 PHE A 652 TRP 0.016 0.001 TRP A 665 HIS 0.004 0.001 HIS A 845 Details of bonding type rmsd covalent geometry : bond 0.00282 (12039) covalent geometry : angle 0.46126 (16167) SS BOND : bond 0.00349 ( 27) SS BOND : angle 0.89430 ( 54) hydrogen bonds : bond 0.03422 ( 609) hydrogen bonds : angle 3.43330 ( 1800) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 675 LEU cc_start: 0.5161 (tp) cc_final: 0.4887 (mt) REVERT: A 683 LYS cc_start: 0.8428 (tppt) cc_final: 0.7738 (tptp) REVERT: A 836 ASP cc_start: 0.8171 (t70) cc_final: 0.7749 (t0) REVERT: A 844 LYS cc_start: 0.7261 (tttm) cc_final: 0.6863 (mmmt) REVERT: A 1093 CYS cc_start: 0.5221 (p) cc_final: 0.4947 (p) REVERT: A 1269 THR cc_start: 0.6804 (p) cc_final: 0.6038 (t) REVERT: A 1731 ASP cc_start: 0.7150 (p0) cc_final: 0.6921 (p0) REVERT: A 1935 GLU cc_start: 0.6508 (tp30) cc_final: 0.6265 (tm-30) outliers start: 10 outliers final: 9 residues processed: 132 average time/residue: 0.1905 time to fit residues: 36.7520 Evaluate side-chains 128 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 784 ASN Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain A residue 813 PHE Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1915 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 0.0370 chunk 132 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1027 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.275857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.265830 restraints weight = 38509.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.262558 restraints weight = 49826.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.260343 restraints weight = 43475.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.259819 restraints weight = 44696.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.259816 restraints weight = 30666.698| |-----------------------------------------------------------------------------| r_work (final): 0.4642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5727 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12066 Z= 0.119 Angle : 0.454 10.323 16221 Z= 0.246 Chirality : 0.055 1.719 1666 Planarity : 0.003 0.037 2068 Dihedral : 3.188 20.012 1545 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.92 % Allowed : 10.20 % Favored : 88.88 % 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: 0.50 (0.23), residues: 1381 helix: 2.26 (0.19), residues: 816 sheet: None (None), residues: 0 loop : -2.82 (0.22), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1895 TYR 0.015 0.001 TYR A1867 PHE 0.016 0.001 PHE A 652 TRP 0.014 0.001 TRP A 665 HIS 0.003 0.001 HIS A1787 Details of bonding type rmsd covalent geometry : bond 0.00270 (12039) covalent geometry : angle 0.45157 (16167) SS BOND : bond 0.00320 ( 27) SS BOND : angle 0.91963 ( 54) hydrogen bonds : bond 0.03273 ( 609) hydrogen bonds : angle 3.36486 ( 1800) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 683 LYS cc_start: 0.8412 (tppt) cc_final: 0.7810 (tptp) REVERT: A 836 ASP cc_start: 0.8128 (t70) cc_final: 0.7766 (t0) REVERT: A 844 LYS cc_start: 0.7319 (tttm) cc_final: 0.6876 (tmtt) REVERT: A 921 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8274 (t) REVERT: A 1039 ASN cc_start: 0.7348 (p0) cc_final: 0.6942 (t0) REVERT: A 1269 THR cc_start: 0.6682 (p) cc_final: 0.5906 (t) REVERT: A 1731 ASP cc_start: 0.7119 (p0) cc_final: 0.6750 (p0) outliers start: 12 outliers final: 8 residues processed: 128 average time/residue: 0.1858 time to fit residues: 34.8109 Evaluate side-chains 124 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain A residue 813 PHE Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 1915 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 107 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 50 optimal weight: 0.0670 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 ASN ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.270870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.261059 restraints weight = 37565.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.258079 restraints weight = 45139.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.255696 restraints weight = 47058.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.254343 restraints weight = 48904.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.252687 restraints weight = 44397.396| |-----------------------------------------------------------------------------| r_work (final): 0.4579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5782 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12066 Z= 0.128 Angle : 0.465 10.298 16221 Z= 0.253 Chirality : 0.055 1.720 1666 Planarity : 0.003 0.037 2068 Dihedral : 3.276 19.478 1545 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.30 % Allowed : 11.12 % Favored : 87.58 % 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: 0.41 (0.23), residues: 1381 helix: 2.19 (0.18), residues: 821 sheet: None (None), residues: 0 loop : -2.92 (0.22), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1895 TYR 0.015 0.001 TYR A1867 PHE 0.017 0.001 PHE A 652 TRP 0.014 0.001 TRP A 665 HIS 0.004 0.001 HIS A 845 Details of bonding type rmsd covalent geometry : bond 0.00292 (12039) covalent geometry : angle 0.46305 (16167) SS BOND : bond 0.00377 ( 27) SS BOND : angle 0.85934 ( 54) hydrogen bonds : bond 0.03333 ( 609) hydrogen bonds : angle 3.40624 ( 1800) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 683 LYS cc_start: 0.8536 (tppt) cc_final: 0.7998 (tptp) REVERT: A 767 VAL cc_start: 0.6732 (OUTLIER) cc_final: 0.6523 (t) REVERT: A 836 ASP cc_start: 0.8159 (t70) cc_final: 0.7859 (t0) REVERT: A 844 LYS cc_start: 0.7407 (tttm) cc_final: 0.6899 (tmtt) REVERT: A 921 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8278 (t) REVERT: A 955 ASN cc_start: 0.7417 (OUTLIER) cc_final: 0.6730 (t0) REVERT: A 1039 ASN cc_start: 0.7470 (p0) cc_final: 0.7130 (t0) REVERT: A 1146 PHE cc_start: 0.6466 (t80) cc_final: 0.6165 (t80) REVERT: A 1269 THR cc_start: 0.6787 (p) cc_final: 0.6159 (t) REVERT: A 1351 PHE cc_start: 0.7801 (t80) cc_final: 0.7513 (t80) REVERT: A 1731 ASP cc_start: 0.7267 (p0) cc_final: 0.6935 (p0) outliers start: 17 outliers final: 7 residues processed: 139 average time/residue: 0.1992 time to fit residues: 40.3006 Evaluate side-chains 133 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 785 CYS Chi-restraints excluded: chain A residue 813 PHE Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 955 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 124 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 118 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 ASN ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN A1027 ASN A1674 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.268777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.263875 restraints weight = 37430.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.262612 restraints weight = 48923.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.260860 restraints weight = 51089.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.260455 restraints weight = 48860.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.258975 restraints weight = 41400.061| |-----------------------------------------------------------------------------| r_work (final): 0.4661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5728 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12066 Z= 0.147 Angle : 0.493 10.269 16221 Z= 0.270 Chirality : 0.055 1.722 1666 Planarity : 0.003 0.038 2068 Dihedral : 3.461 20.582 1545 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.69 % Allowed : 12.50 % Favored : 85.81 % 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: 0.33 (0.23), residues: 1381 helix: 2.10 (0.18), residues: 822 sheet: -0.10 (2.22), residues: 10 loop : -2.96 (0.22), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 761 TYR 0.019 0.001 TYR A1867 PHE 0.019 0.001 PHE A 652 TRP 0.015 0.001 TRP A 665 HIS 0.004 0.001 HIS A 845 Details of bonding type rmsd covalent geometry : bond 0.00334 (12039) covalent geometry : angle 0.49077 (16167) SS BOND : bond 0.00349 ( 27) SS BOND : angle 1.01676 ( 54) hydrogen bonds : bond 0.03485 ( 609) hydrogen bonds : angle 3.50037 ( 1800) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 ASN cc_start: 0.4868 (OUTLIER) cc_final: 0.4644 (t0) REVERT: A 683 LYS cc_start: 0.8424 (tppt) cc_final: 0.7891 (tptp) REVERT: A 836 ASP cc_start: 0.8180 (t70) cc_final: 0.7929 (t0) REVERT: A 844 LYS cc_start: 0.7604 (tttm) cc_final: 0.7058 (tmtt) REVERT: A 955 ASN cc_start: 0.7463 (OUTLIER) cc_final: 0.6783 (t0) REVERT: A 1039 ASN cc_start: 0.7528 (OUTLIER) cc_final: 0.7226 (t0) REVERT: A 1146 PHE cc_start: 0.6350 (t80) cc_final: 0.5993 (t80) REVERT: A 1269 THR cc_start: 0.6409 (p) cc_final: 0.6064 (t) REVERT: A 1731 ASP cc_start: 0.7067 (p0) cc_final: 0.6803 (p0) outliers start: 22 outliers final: 10 residues processed: 145 average time/residue: 0.2006 time to fit residues: 42.6106 Evaluate side-chains 140 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 813 PHE Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1039 ASN Chi-restraints excluded: chain A residue 1093 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 139 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN A1794 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.268464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.263195 restraints weight = 37353.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.236649 restraints weight = 57614.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.232884 restraints weight = 59223.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.233488 restraints weight = 49348.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.233666 restraints weight = 34955.958| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12066 Z= 0.142 Angle : 0.487 10.279 16221 Z= 0.266 Chirality : 0.055 1.720 1666 Planarity : 0.003 0.039 2068 Dihedral : 3.466 20.782 1545 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.15 % Allowed : 13.80 % Favored : 85.05 % 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: 0.26 (0.23), residues: 1381 helix: 2.06 (0.18), residues: 821 sheet: None (None), residues: 0 loop : -2.97 (0.22), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 761 TYR 0.016 0.001 TYR A1867 PHE 0.018 0.001 PHE A 652 TRP 0.020 0.001 TRP A1103 HIS 0.005 0.001 HIS A1787 Details of bonding type rmsd covalent geometry : bond 0.00324 (12039) covalent geometry : angle 0.48368 (16167) SS BOND : bond 0.00378 ( 27) SS BOND : angle 1.05254 ( 54) hydrogen bonds : bond 0.03472 ( 609) hydrogen bonds : angle 3.54074 ( 1800) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 683 LYS cc_start: 0.8523 (tppt) cc_final: 0.8069 (tptp) REVERT: A 836 ASP cc_start: 0.8206 (t70) cc_final: 0.7957 (t0) REVERT: A 844 LYS cc_start: 0.7609 (tttm) cc_final: 0.7044 (tmtt) REVERT: A 955 ASN cc_start: 0.7382 (OUTLIER) cc_final: 0.6894 (t0) REVERT: A 1039 ASN cc_start: 0.7353 (OUTLIER) cc_final: 0.7110 (t0) REVERT: A 1146 PHE cc_start: 0.6771 (t80) cc_final: 0.6368 (t80) REVERT: A 1269 THR cc_start: 0.7231 (p) cc_final: 0.6819 (t) REVERT: A 1731 ASP cc_start: 0.7450 (p0) cc_final: 0.7186 (p0) REVERT: A 1905 ILE cc_start: 0.7691 (mt) cc_final: 0.7393 (mt) outliers start: 15 outliers final: 9 residues processed: 139 average time/residue: 0.2027 time to fit residues: 40.7639 Evaluate side-chains 133 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 813 PHE Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1039 ASN Chi-restraints excluded: chain A residue 1093 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 105 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 118 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 116 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 ASN A 676 ASN ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN ** A1776 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 = 0.4768 r_free = 0.4768 target = 0.270081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.264984 restraints weight = 37345.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.263845 restraints weight = 56446.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.245571 restraints weight = 56275.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.238380 restraints weight = 42030.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.237853 restraints weight = 38891.058| |-----------------------------------------------------------------------------| r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12066 Z= 0.106 Angle : 0.459 10.263 16221 Z= 0.247 Chirality : 0.055 1.719 1666 Planarity : 0.003 0.040 2068 Dihedral : 3.312 19.109 1545 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.38 % Allowed : 13.96 % Favored : 84.66 % 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: 0.42 (0.23), residues: 1381 helix: 2.19 (0.18), residues: 822 sheet: None (None), residues: 0 loop : -2.92 (0.22), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 761 TYR 0.012 0.001 TYR A1867 PHE 0.014 0.001 PHE A 652 TRP 0.016 0.001 TRP A1103 HIS 0.006 0.001 HIS A1787 Details of bonding type rmsd covalent geometry : bond 0.00240 (12039) covalent geometry : angle 0.45471 (16167) SS BOND : bond 0.00365 ( 27) SS BOND : angle 1.13349 ( 54) hydrogen bonds : bond 0.03240 ( 609) hydrogen bonds : angle 3.36111 ( 1800) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7172 (mt) REVERT: A 683 LYS cc_start: 0.8545 (tppt) cc_final: 0.8116 (tptp) REVERT: A 836 ASP cc_start: 0.8133 (t70) cc_final: 0.7869 (t0) REVERT: A 844 LYS cc_start: 0.7382 (tttm) cc_final: 0.6813 (tmtt) REVERT: A 1146 PHE cc_start: 0.6676 (t80) cc_final: 0.6274 (t80) REVERT: A 1269 THR cc_start: 0.7225 (p) cc_final: 0.6737 (t) REVERT: A 1731 ASP cc_start: 0.7527 (p0) cc_final: 0.7251 (p0) REVERT: A 1905 ILE cc_start: 0.7769 (mt) cc_final: 0.7453 (mt) outliers start: 18 outliers final: 12 residues processed: 137 average time/residue: 0.2158 time to fit residues: 42.4018 Evaluate side-chains 134 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 813 PHE Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1093 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 59 optimal weight: 0.0570 chunk 16 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 26 optimal weight: 30.0000 chunk 58 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN ** A1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1043 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1794 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.267054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.262084 restraints weight = 36705.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.260769 restraints weight = 49020.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.240310 restraints weight = 56282.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.234074 restraints weight = 52284.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.234430 restraints weight = 44010.791| |-----------------------------------------------------------------------------| r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12066 Z= 0.142 Angle : 0.491 10.267 16221 Z= 0.267 Chirality : 0.055 1.721 1666 Planarity : 0.003 0.045 2068 Dihedral : 3.414 20.012 1545 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 1.00 % Allowed : 14.80 % Favored : 84.20 % 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: 0.32 (0.23), residues: 1381 helix: 2.12 (0.18), residues: 822 sheet: None (None), residues: 0 loop : -2.96 (0.22), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 761 TYR 0.016 0.001 TYR A1867 PHE 0.017 0.001 PHE A 652 TRP 0.014 0.001 TRP A 665 HIS 0.005 0.001 HIS A1787 Details of bonding type rmsd covalent geometry : bond 0.00327 (12039) covalent geometry : angle 0.48710 (16167) SS BOND : bond 0.00376 ( 27) SS BOND : angle 1.21588 ( 54) hydrogen bonds : bond 0.03401 ( 609) hydrogen bonds : angle 3.44952 ( 1800) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7161 (mt) REVERT: A 683 LYS cc_start: 0.8548 (tppt) cc_final: 0.8123 (tptp) REVERT: A 836 ASP cc_start: 0.8232 (t70) cc_final: 0.7988 (t0) REVERT: A 844 LYS cc_start: 0.7536 (tttm) cc_final: 0.6963 (tmtt) REVERT: A 955 ASN cc_start: 0.7293 (OUTLIER) cc_final: 0.6825 (t0) REVERT: A 1146 PHE cc_start: 0.6686 (t80) cc_final: 0.6322 (t80) REVERT: A 1269 THR cc_start: 0.7066 (p) cc_final: 0.6402 (t) REVERT: A 1731 ASP cc_start: 0.7488 (p0) cc_final: 0.7240 (p0) REVERT: A 1783 MET cc_start: 0.6768 (tpt) cc_final: 0.6161 (tpp) REVERT: A 1905 ILE cc_start: 0.7718 (mt) cc_final: 0.7401 (mt) outliers start: 13 outliers final: 11 residues processed: 135 average time/residue: 0.2107 time to fit residues: 40.6163 Evaluate side-chains 135 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 813 PHE Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1541 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 19 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 24 optimal weight: 30.0000 chunk 86 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN A1027 ASN A1659 GLN ** A1923 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 = 0.4680 r_free = 0.4680 target = 0.259112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.253862 restraints weight = 37004.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.252399 restraints weight = 49251.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.233019 restraints weight = 51678.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.226547 restraints weight = 47485.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.226843 restraints weight = 41837.688| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 12066 Z= 0.244 Angle : 0.641 10.287 16221 Z= 0.358 Chirality : 0.059 1.726 1666 Planarity : 0.004 0.059 2068 Dihedral : 4.121 29.398 1545 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 1.38 % Allowed : 14.65 % Favored : 83.97 % 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: -0.29 (0.23), residues: 1381 helix: 1.62 (0.18), residues: 824 sheet: -0.74 (2.09), residues: 10 loop : -3.27 (0.21), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 761 TYR 0.026 0.002 TYR A1867 PHE 0.029 0.002 PHE A 652 TRP 0.019 0.002 TRP A 665 HIS 0.006 0.001 HIS A 845 Details of bonding type rmsd covalent geometry : bond 0.00564 (12039) covalent geometry : angle 0.63651 (16167) SS BOND : bond 0.00541 ( 27) SS BOND : angle 1.39384 ( 54) hydrogen bonds : bond 0.04331 ( 609) hydrogen bonds : angle 3.97853 ( 1800) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2762 Ramachandran restraints generated. 1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 683 LYS cc_start: 0.8489 (tppt) cc_final: 0.8116 (tptp) REVERT: A 844 LYS cc_start: 0.7780 (tttm) cc_final: 0.7115 (mmmt) REVERT: A 919 THR cc_start: 0.7210 (p) cc_final: 0.6924 (p) REVERT: A 1146 PHE cc_start: 0.6686 (t80) cc_final: 0.6403 (t80) REVERT: A 1783 MET cc_start: 0.7066 (tpt) cc_final: 0.6620 (tpp) REVERT: A 1905 ILE cc_start: 0.8033 (mt) cc_final: 0.7755 (mt) outliers start: 18 outliers final: 14 residues processed: 155 average time/residue: 0.2121 time to fit residues: 47.1937 Evaluate side-chains 150 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 813 PHE Chi-restraints excluded: chain A residue 814 ILE Chi-restraints excluded: chain A residue 815 GLU Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1093 CYS Chi-restraints excluded: chain A residue 1541 GLU Chi-restraints excluded: chain A residue 1691 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 105 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 75 optimal weight: 0.2980 chunk 92 optimal weight: 6.9990 chunk 113 optimal weight: 0.3980 chunk 24 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN A1794 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.266028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.261006 restraints weight = 36886.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.259305 restraints weight = 51081.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.258016 restraints weight = 49267.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.257062 restraints weight = 46091.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.255423 restraints weight = 44893.903| |-----------------------------------------------------------------------------| r_work (final): 0.4646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5782 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12066 Z= 0.111 Angle : 0.492 10.272 16221 Z= 0.266 Chirality : 0.055 1.718 1666 Planarity : 0.003 0.048 2068 Dihedral : 3.640 19.725 1545 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.84 % Allowed : 15.72 % Favored : 83.44 % 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 (0.23), residues: 1381 helix: 1.96 (0.18), residues: 820 sheet: None (None), residues: 0 loop : -3.06 (0.22), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 631 TYR 0.013 0.001 TYR A1867 PHE 0.014 0.001 PHE A 652 TRP 0.018 0.001 TRP A1103 HIS 0.008 0.001 HIS A1787 Details of bonding type rmsd covalent geometry : bond 0.00251 (12039) covalent geometry : angle 0.48863 (16167) SS BOND : bond 0.00330 ( 27) SS BOND : angle 1.16153 ( 54) hydrogen bonds : bond 0.03508 ( 609) hydrogen bonds : angle 3.50310 ( 1800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2635.59 seconds wall clock time: 46 minutes 7.20 seconds (2767.20 seconds total)