Starting phenix.real_space_refine on Sat Sep 28 21:34:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jge_22324/09_2024/7jge_22324.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jge_22324/09_2024/7jge_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jge_22324/09_2024/7jge_22324.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jge_22324/09_2024/7jge_22324.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jge_22324/09_2024/7jge_22324.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jge_22324/09_2024/7jge_22324.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 9.51, per 1000 atoms: 0.47 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: 5.41 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.61 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: 6.71 Time building geometry restraints manager: 6.46 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: 0.970 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: 0.340 Extract box with map and model: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 42.350 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.980 ------------------------------------------------------------------------------- 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 12039 Z= 0.110 Angle : 0.439 10.499 16167 Z= 0.256 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 : 14.01 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.001 TRP A 665 HIS 0.004 0.001 HIS A 845 PHE 0.007 0.001 PHE A 652 TYR 0.009 0.001 TYR A 588 ARG 0.002 0.000 ARG A 851 *********************** 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 fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.641 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: 0.3898 time to fit residues: 73.4737 Evaluate side-chains 110 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 112 optimal weight: 0.0050 chunk 43 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN A 845 HIS ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1368 HIS A1424 ASN A1522 GLN A1586 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5515 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12039 Z= 0.180 Angle : 0.457 10.471 16167 Z= 0.248 Chirality : 0.054 1.709 1666 Planarity : 0.003 0.037 2068 Dihedral : 2.842 21.455 1545 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.61 % Allowed : 5.90 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.24), residues: 1381 helix: 2.47 (0.19), residues: 812 sheet: 1.11 (2.00), residues: 10 loop : -2.72 (0.23), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 560 HIS 0.003 0.001 HIS A1787 PHE 0.015 0.001 PHE A 652 TYR 0.016 0.001 TYR A 810 ARG 0.002 0.000 ARG A1349 *********************** 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 133 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 1.621 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: A 836 ASP cc_start: 0.7895 (t70) cc_final: 0.7407 (t0) REVERT: A 844 LYS cc_start: 0.6992 (tttm) cc_final: 0.6689 (mmmt) REVERT: A 1730 ASN cc_start: 0.5770 (t0) cc_final: 0.5034 (m-40) REVERT: A 1731 ASP cc_start: 0.6709 (p0) cc_final: 0.5861 (p0) REVERT: A 1935 GLU cc_start: 0.6379 (tp30) cc_final: 0.6054 (tm-30) outliers start: 8 outliers final: 6 residues processed: 129 average time/residue: 0.4240 time to fit residues: 80.0425 Evaluate side-chains 124 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 1.614 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 A1037 GLN A1048 GLN A1794 GLN A1857 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5628 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12039 Z= 0.189 Angle : 0.459 10.411 16167 Z= 0.250 Chirality : 0.055 1.718 1666 Planarity : 0.003 0.048 2068 Dihedral : 3.118 21.332 1545 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.61 % Allowed : 8.05 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.24), residues: 1381 helix: 2.34 (0.19), residues: 812 sheet: 1.04 (1.97), residues: 10 loop : -2.71 (0.23), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 665 HIS 0.004 0.001 HIS A 845 PHE 0.017 0.001 PHE A 652 TYR 0.015 0.001 TYR A1867 ARG 0.005 0.000 ARG A1895 *********************** 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 132 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 1.717 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: A 675 LEU cc_start: 0.5068 (tp) cc_final: 0.4803 (mt) REVERT: A 836 ASP cc_start: 0.8086 (t70) cc_final: 0.7667 (t0) REVERT: A 844 LYS cc_start: 0.7142 (tttm) cc_final: 0.6813 (tptp) REVERT: A 1093 CYS cc_start: 0.4743 (p) cc_final: 0.4530 (p) REVERT: A 1269 THR cc_start: 0.6409 (p) cc_final: 0.5763 (t) REVERT: A 1730 ASN cc_start: 0.5835 (t0) cc_final: 0.5100 (m-40) REVERT: A 1731 ASP cc_start: 0.6652 (p0) cc_final: 0.6007 (p0) REVERT: A 1935 GLU cc_start: 0.6367 (tp30) cc_final: 0.6165 (tm-30) outliers start: 8 outliers final: 7 residues processed: 128 average time/residue: 0.4362 time to fit residues: 81.7716 Evaluate side-chains 122 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 THR 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 128 optimal weight: 4.9990 chunk 97 optimal weight: 0.0770 chunk 67 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN A 845 HIS ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1424 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5651 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12039 Z= 0.153 Angle : 0.433 10.389 16167 Z= 0.234 Chirality : 0.054 1.718 1666 Planarity : 0.002 0.038 2068 Dihedral : 3.025 19.277 1545 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.69 % Allowed : 9.28 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.24), residues: 1381 helix: 2.41 (0.19), residues: 816 sheet: 0.75 (1.91), residues: 10 loop : -2.78 (0.23), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 665 HIS 0.003 0.001 HIS A1787 PHE 0.014 0.001 PHE A 652 TYR 0.012 0.001 TYR A1867 ARG 0.004 0.000 ARG A1895 *********************** 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 127 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 1.762 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 836 ASP cc_start: 0.8088 (t70) cc_final: 0.7682 (t0) REVERT: A 844 LYS cc_start: 0.7098 (tttm) cc_final: 0.6837 (mmmt) REVERT: A 1269 THR cc_start: 0.6621 (p) cc_final: 0.5997 (t) REVERT: A 1731 ASP cc_start: 0.7006 (p0) cc_final: 0.6604 (p0) REVERT: A 1935 GLU cc_start: 0.6394 (tp30) cc_final: 0.6162 (tm-30) outliers start: 9 outliers final: 6 residues processed: 123 average time/residue: 0.4222 time to fit residues: 77.8205 Evaluate side-chains 118 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 785 CYS Chi-restraints excluded: chain A residue 813 PHE 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 115 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 2 optimal weight: 0.0870 chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN A1027 ASN A1424 ASN A1659 GLN A1674 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5903 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12039 Z= 0.307 Angle : 0.583 10.306 16167 Z= 0.327 Chirality : 0.057 1.723 1666 Planarity : 0.004 0.039 2068 Dihedral : 3.860 24.299 1545 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 1.69 % Allowed : 9.82 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.23), residues: 1381 helix: 1.82 (0.18), residues: 818 sheet: -0.46 (1.98), residues: 10 loop : -3.03 (0.21), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 665 HIS 0.004 0.001 HIS A1897 PHE 0.026 0.002 PHE A 652 TYR 0.024 0.002 TYR A1867 ARG 0.006 0.001 ARG A 231 *********************** 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 158 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 136 time to evaluate : 1.748 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: A 774 ARG cc_start: 0.7516 (ttt-90) cc_final: 0.7309 (ttt90) REVERT: A 844 LYS cc_start: 0.7811 (tttm) cc_final: 0.6563 (mptt) REVERT: A 1146 PHE cc_start: 0.6533 (t80) cc_final: 0.6257 (t80) REVERT: A 1731 ASP cc_start: 0.7196 (p0) cc_final: 0.6927 (p0) REVERT: A 1905 ILE cc_start: 0.7725 (mt) cc_final: 0.7481 (mt) outliers start: 22 outliers final: 16 residues processed: 150 average time/residue: 0.4279 time to fit residues: 93.9127 Evaluate side-chains 136 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.743 ------------------------------------------------------------------------------- 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 781 VAL 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 1010 VAL Chi-restraints excluded: chain A residue 1039 ASN Chi-restraints excluded: chain A residue 1093 CYS Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1866 ILE Chi-restraints excluded: chain A residue 1915 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 81 optimal weight: 0.0270 chunk 34 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 11 optimal weight: 30.0000 chunk 45 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 ASN ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN A1794 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5815 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12039 Z= 0.161 Angle : 0.463 10.326 16167 Z= 0.252 Chirality : 0.055 1.718 1666 Planarity : 0.003 0.041 2068 Dihedral : 3.459 19.293 1545 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.23 % Allowed : 11.81 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.23), residues: 1381 helix: 2.03 (0.18), residues: 824 sheet: None (None), residues: 0 loop : -2.96 (0.22), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 665 HIS 0.003 0.001 HIS A 845 PHE 0.016 0.001 PHE A 652 TYR 0.014 0.001 TYR A1867 ARG 0.003 0.000 ARG A 761 *********************** 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 141 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 1.672 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: A 836 ASP cc_start: 0.8189 (t70) cc_final: 0.7920 (t0) REVERT: A 844 LYS cc_start: 0.7571 (tttm) cc_final: 0.7051 (tmtt) REVERT: A 955 ASN cc_start: 0.7250 (OUTLIER) cc_final: 0.6864 (t0) REVERT: A 1039 ASN cc_start: 0.7424 (p0) cc_final: 0.7129 (t0) REVERT: A 1146 PHE cc_start: 0.6471 (t80) cc_final: 0.6073 (t80) REVERT: A 1269 THR cc_start: 0.6519 (p) cc_final: 0.5927 (t) REVERT: A 1731 ASP cc_start: 0.7200 (p0) cc_final: 0.6942 (p0) outliers start: 16 outliers final: 8 residues processed: 136 average time/residue: 0.4270 time to fit residues: 85.7531 Evaluate side-chains 132 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 1.717 ------------------------------------------------------------------------------- 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 845 HIS Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1104 ILE Chi-restraints excluded: chain A residue 1915 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN ** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN A1794 GLN A1911 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5990 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 12039 Z= 0.350 Angle : 0.599 10.261 16167 Z= 0.337 Chirality : 0.058 1.724 1666 Planarity : 0.004 0.047 2068 Dihedral : 3.985 26.719 1545 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 1.84 % Allowed : 12.50 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.23), residues: 1381 helix: 1.69 (0.18), residues: 822 sheet: -0.53 (2.12), residues: 10 loop : -3.22 (0.21), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 665 HIS 0.005 0.001 HIS A1787 PHE 0.027 0.002 PHE A 652 TYR 0.026 0.002 TYR A1867 ARG 0.007 0.001 ARG A 761 *********************** 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 162 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 1.726 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: A 765 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6580 (tp30) REVERT: A 844 LYS cc_start: 0.7748 (tttm) cc_final: 0.6483 (mptt) REVERT: A 1146 PHE cc_start: 0.6620 (t80) cc_final: 0.6307 (t80) REVERT: A 1731 ASP cc_start: 0.7233 (p0) cc_final: 0.7032 (p0) outliers start: 24 outliers final: 15 residues processed: 158 average time/residue: 0.4266 time to fit residues: 99.1393 Evaluate side-chains 146 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 1.728 ------------------------------------------------------------------------------- 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 719 ILE Chi-restraints excluded: chain A residue 765 GLU 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 921 THR Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1046 ILE Chi-restraints excluded: chain A residue 1093 CYS Chi-restraints excluded: chain A residue 1691 ILE Chi-restraints excluded: chain A residue 1915 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.5980 chunk 82 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN A 635 ASN ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN A1027 ASN ** A1776 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1794 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5930 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12039 Z= 0.223 Angle : 0.510 10.269 16167 Z= 0.281 Chirality : 0.056 1.720 1666 Planarity : 0.003 0.045 2068 Dihedral : 3.789 22.718 1545 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.53 % Allowed : 14.03 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.23), residues: 1381 helix: 1.79 (0.18), residues: 824 sheet: None (None), residues: 0 loop : -3.15 (0.21), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1103 HIS 0.005 0.001 HIS A1787 PHE 0.019 0.002 PHE A 652 TYR 0.018 0.001 TYR A1867 ARG 0.005 0.000 ARG A 761 *********************** 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 153 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 1.638 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: A 755 LEU cc_start: 0.5928 (mt) cc_final: 0.5722 (pp) REVERT: A 844 LYS cc_start: 0.7656 (tttm) cc_final: 0.7087 (tmtt) REVERT: A 1146 PHE cc_start: 0.6488 (t80) cc_final: 0.6189 (t80) REVERT: A 1731 ASP cc_start: 0.7265 (p0) cc_final: 0.7063 (p0) REVERT: A 1783 MET cc_start: 0.7008 (tpt) cc_final: 0.6537 (tpp) outliers start: 20 outliers final: 15 residues processed: 148 average time/residue: 0.4226 time to fit residues: 92.2626 Evaluate side-chains 147 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.635 ------------------------------------------------------------------------------- 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 635 ASN 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 845 HIS Chi-restraints excluded: chain A residue 919 THR 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 1039 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 128 optimal weight: 0.1980 chunk 77 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5888 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12039 Z= 0.162 Angle : 0.478 10.261 16167 Z= 0.260 Chirality : 0.055 1.719 1666 Planarity : 0.003 0.042 2068 Dihedral : 3.615 19.329 1545 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.92 % Allowed : 14.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1381 helix: 2.01 (0.18), residues: 821 sheet: None (None), residues: 0 loop : -3.08 (0.22), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1103 HIS 0.005 0.001 HIS A1787 PHE 0.015 0.001 PHE A 652 TYR 0.014 0.001 TYR A1867 ARG 0.004 0.000 ARG A 761 *********************** 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 144 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 1.861 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 755 LEU cc_start: 0.5977 (mt) cc_final: 0.5699 (pp) REVERT: A 836 ASP cc_start: 0.8206 (t70) cc_final: 0.7969 (t0) REVERT: A 844 LYS cc_start: 0.7548 (tttm) cc_final: 0.7017 (tmtt) REVERT: A 955 ASN cc_start: 0.7318 (OUTLIER) cc_final: 0.6922 (t0) REVERT: A 1146 PHE cc_start: 0.6436 (t80) cc_final: 0.6137 (t80) REVERT: A 1731 ASP cc_start: 0.7299 (p0) cc_final: 0.7093 (p0) REVERT: A 1783 MET cc_start: 0.6978 (tpt) cc_final: 0.6496 (tpp) outliers start: 12 outliers final: 11 residues processed: 142 average time/residue: 0.4366 time to fit residues: 91.0947 Evaluate side-chains 141 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.692 ------------------------------------------------------------------------------- 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 635 ASN 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 845 HIS Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 973 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 135 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 113 optimal weight: 0.0870 chunk 11 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12039 Z= 0.213 Angle : 0.506 10.241 16167 Z= 0.277 Chirality : 0.056 1.722 1666 Planarity : 0.003 0.044 2068 Dihedral : 3.665 21.534 1545 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.15 % Allowed : 14.34 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.23), residues: 1381 helix: 1.97 (0.18), residues: 821 sheet: None (None), residues: 0 loop : -3.11 (0.22), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 665 HIS 0.006 0.001 HIS A1787 PHE 0.017 0.001 PHE A 652 TYR 0.017 0.001 TYR A1867 ARG 0.005 0.000 ARG A 761 ********************** 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 143 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.766 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 570 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7434 (mt) REVERT: A 755 LEU cc_start: 0.5879 (mt) cc_final: 0.5582 (pp) REVERT: A 844 LYS cc_start: 0.7613 (tttm) cc_final: 0.6454 (mptt) REVERT: A 955 ASN cc_start: 0.7424 (OUTLIER) cc_final: 0.6898 (t0) REVERT: A 1146 PHE cc_start: 0.6520 (t80) cc_final: 0.6226 (t80) REVERT: A 1158 PHE cc_start: 0.7158 (m-80) cc_final: 0.6869 (m-80) REVERT: A 1783 MET cc_start: 0.7015 (tpt) cc_final: 0.6552 (tpp) outliers start: 15 outliers final: 13 residues processed: 141 average time/residue: 0.4649 time to fit residues: 97.2466 Evaluate side-chains 143 residues out of total 1306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.744 ------------------------------------------------------------------------------- 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 635 ASN 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 845 HIS Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 921 THR 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 1691 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.265777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.260345 restraints weight = 37173.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.227730 restraints weight = 55704.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.226512 restraints weight = 53575.299| |-----------------------------------------------------------------------------| r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12039 Z= 0.192 Angle : 0.491 10.242 16167 Z= 0.269 Chirality : 0.055 1.721 1666 Planarity : 0.003 0.043 2068 Dihedral : 3.629 20.071 1545 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 1.15 % Allowed : 14.42 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.23), residues: 1381 helix: 1.99 (0.18), residues: 821 sheet: None (None), residues: 0 loop : -3.09 (0.22), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 665 HIS 0.005 0.001 HIS A1787 PHE 0.017 0.001 PHE A 652 TYR 0.016 0.001 TYR A1867 ARG 0.004 0.000 ARG A 761 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3613.06 seconds wall clock time: 64 minutes 30.92 seconds (3870.92 seconds total)