Starting phenix.real_space_refine on Sun Sep 13 01:38:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jgh_22327/09_2026/7jgh_22327.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jgh_22327/09_2026/7jgh_22327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7jgh_22327/09_2026/7jgh_22327.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jgh_22327/09_2026/7jgh_22327.cif" model { file = "/net/cci-nas-00/data/ceres_data/7jgh_22327/09_2026/7jgh_22327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jgh_22327/09_2026/7jgh_22327.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jgh_22327/09_2026/7jgh_22327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jgh_22327/09_2026/7jgh_22327.map" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 92 5.16 5 C 7462 2.51 5 N 2007 2.21 5 O 2322 1.98 5 H 7725 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.24s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19608 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 19428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1421, 19428 Classifications: {'peptide': 1421} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 40, 'TRANS': 1380} Chain breaks: 28 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 162 Unusual residues: {'ASG': 5, 'BDP': 6} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'ASG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" C1 BDP B 1 " occ=0.93 ... (11 atoms not shown) pdb=" O6B BDP B 1 " occ=0.93 residue: pdb=" C1 ASG B 2 " occ=0.93 ... (16 atoms not shown) pdb=" S ASG B 2 " occ=0.93 residue: pdb=" C1 BDP B 3 " occ=0.93 ... (10 atoms not shown) pdb=" O6B BDP B 3 " occ=0.93 residue: pdb=" C1 ASG B 4 " occ=0.93 ... (16 atoms not shown) pdb=" S ASG B 4 " occ=0.93 residue: pdb=" C1 BDP B 5 " occ=0.93 ... (10 atoms not shown) pdb=" O6B BDP B 5 " occ=0.93 residue: pdb=" C1 ASG B 6 " occ=0.93 ... (16 atoms not shown) pdb=" S ASG B 6 " occ=0.93 residue: pdb=" C1 BDP B 7 " occ=0.93 ... (10 atoms not shown) pdb=" O6B BDP B 7 " occ=0.93 residue: pdb=" C1 ASG B 8 " occ=0.93 ... (16 atoms not shown) pdb=" S ASG B 8 " occ=0.93 residue: pdb=" C1 BDP B 9 " occ=0.93 ... (10 atoms not shown) pdb=" O6B BDP B 9 " occ=0.93 residue: pdb=" C1 ASG B 10 " occ=0.93 ... (16 atoms not shown) pdb=" S ASG B 10 " occ=0.93 residue: pdb=" C1 BDP B 11 " occ=0.93 ... (9 atoms not shown) pdb=" O6B BDP B 11 " occ=0.93 residue: pdb=" C1 ASG A2701 " occ=0.93 ... (16 atoms not shown) pdb=" S ASG A2701 " occ=0.93 Time building chain proxies: 3.87, per 1000 atoms: 0.20 Number of scatterers: 19608 At special positions: 0 Unit cell: (110.032, 132.25, 138.598, 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 92 16.00 O 2322 8.00 N 2007 7.00 C 7462 6.00 H 7725 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 105 " distance=2.04 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 258 " distance=2.03 Simple disulfide: pdb=" SG CYS A 643 " - pdb=" SG CYS A 745 " distance=2.03 Simple disulfide: pdb=" SG CYS A 769 " - pdb=" SG CYS A 901 " distance=2.03 Simple disulfide: pdb=" SG CYS A 783 " - pdb=" SG CYS A 801 " distance=2.03 Simple disulfide: pdb=" SG CYS A 797 " - pdb=" SG CYS A 957 " distance=2.03 Simple disulfide: pdb=" SG CYS A 805 " - pdb=" SG CYS A 955 " distance=2.03 Simple disulfide: pdb=" SG CYS A 966 " - pdb=" SG CYS A1090 " distance=2.03 Simple disulfide: pdb=" SG CYS A 978 " - pdb=" SG CYS A 996 " distance=2.03 Simple disulfide: pdb=" SG CYS A1088 " - pdb=" SG CYS A1193 " distance=2.03 Simple disulfide: pdb=" SG CYS A1140 " - pdb=" SG CYS A1171 " distance=2.03 Simple disulfide: pdb=" SG CYS A1210 " - pdb=" SG CYS A1411 " distance=2.03 Simple disulfide: pdb=" SG CYS A1221 " - pdb=" SG CYS A1264 " distance=2.03 Simple disulfide: pdb=" SG CYS A1242 " - pdb=" SG CYS A1255 " distance=2.04 Simple disulfide: pdb=" SG CYS A1339 " - pdb=" SG CYS A1431 " distance=2.03 Simple disulfide: pdb=" SG CYS A1456 " - pdb=" SG CYS A1528 " distance=2.02 Simple disulfide: pdb=" SG CYS A1470 " - pdb=" SG CYS A1483 " distance=2.03 Simple disulfide: pdb=" SG CYS A1487 " - pdb=" SG CYS A1556 " distance=2.03 Simple disulfide: pdb=" SG CYS A1578 " - pdb=" SG CYS A1614 " distance=2.03 Simple disulfide: pdb=" SG CYS A1670 " - pdb=" SG CYS A1777 " distance=2.03 Simple disulfide: pdb=" SG CYS A1671 " - pdb=" SG CYS A1901 " distance=2.03 Simple disulfide: pdb=" SG CYS A1802 " - pdb=" SG CYS A1904 " distance=2.03 Simple disulfide: pdb=" SG CYS A1816 " - pdb=" SG CYS A1833 " distance=2.03 Simple disulfide: pdb=" SG CYS A1837 " - pdb=" SG CYS A1927 " distance=2.03 Simple disulfide: pdb=" SG CYS A1891 " - pdb=" SG CYS A1902 " 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 Links applied BETA1-3 " ASG B 2 " - " BDP B 3 " " ASG B 4 " - " BDP B 5 " " ASG B 6 " - " BDP B 7 " " ASG B 8 " - " BDP B 9 " " ASG B 10 " - " BDP B 11 " BETA1-4 " BDP B 1 " - " ASG B 2 " " BDP B 3 " - " ASG B 4 " " BDP B 5 " - " ASG B 6 " " BDP B 7 " - " ASG B 8 " " BDP B 9 " - " ASG B 10 " Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 604.5 milliseconds 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2700 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 1 sheets defined 60.7% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 119 through 142 removed outlier: 3.921A pdb=" N PHE A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 165 removed outlier: 4.259A pdb=" N ALA A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.520A pdb=" N GLU A 179 " --> pdb=" O ASN A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 221 Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 273 through 305 removed outlier: 3.656A pdb=" N TRP A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 295 " --> pdb=" O GLN A 291 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 354 Processing helix chain 'A' and resid 363 through 378 Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.972A pdb=" N GLN A 585 " --> pdb=" O PRO A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 636 Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 640 through 659 Processing helix chain 'A' and resid 665 through 683 removed outlier: 4.065A pdb=" N LYS A 669 " --> pdb=" O ASN A 665 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASP A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 722 removed outlier: 4.727A pdb=" N LYS A 715 " --> pdb=" O ASN A 711 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TYR A 716 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 719 " --> pdb=" O LYS A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 782 Proline residue: A 778 - end of helix Processing helix chain 'A' and resid 801 through 813 Processing helix chain 'A' and resid 825 through 847 removed outlier: 3.541A pdb=" N ARG A 829 " --> pdb=" O SER A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 884 removed outlier: 3.682A pdb=" N PHE A 876 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 877 " --> pdb=" O ILE A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 896 Processing helix chain 'A' and resid 961 through 969 removed outlier: 3.818A pdb=" N ARG A 969 " --> pdb=" O THR A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1043 Processing helix chain 'A' and resid 1084 through 1119 Processing helix chain 'A' and resid 1131 through 1149 Processing helix chain 'A' and resid 1160 through 1171 removed outlier: 4.013A pdb=" N CYS A1171 " --> pdb=" O LEU A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1199 Processing helix chain 'A' and resid 1257 through 1262 removed outlier: 3.738A pdb=" N GLN A1261 " --> pdb=" O PRO A1257 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN A1262 " --> pdb=" O PRO A1258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1257 through 1262' Processing helix chain 'A' and resid 1287 through 1309 Processing helix chain 'A' and resid 1337 through 1355 removed outlier: 3.965A pdb=" N ALA A1341 " --> pdb=" O GLY A1337 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1375 removed outlier: 3.571A pdb=" N GLY A1365 " --> pdb=" O TYR A1361 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS A1366 " --> pdb=" O GLU A1362 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU A1367 " --> pdb=" O TYR A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1420 Processing helix chain 'A' and resid 1428 through 1432 removed outlier: 3.657A pdb=" N CYS A1431 " --> pdb=" O ILE A1428 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY A1432 " --> pdb=" O ASP A1429 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1428 through 1432' Processing helix chain 'A' and resid 1443 through 1470 Processing helix chain 'A' and resid 1483 through 1512 Processing helix chain 'A' and resid 1517 through 1525 Processing helix chain 'A' and resid 1532 through 1537 Processing helix chain 'A' and resid 1542 through 1547 Processing helix chain 'A' and resid 1552 through 1558 Processing helix chain 'A' and resid 1609 through 1613 removed outlier: 3.618A pdb=" N LEU A1613 " --> pdb=" O ARG A1610 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1625 removed outlier: 4.343A pdb=" N ILE A1621 " --> pdb=" O GLU A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1631 through 1656 removed outlier: 3.785A pdb=" N GLU A1635 " --> pdb=" O ASN A1631 " (cutoff:3.500A) Processing helix chain 'A' and resid 1662 through 1686 Processing helix chain 'A' and resid 1692 through 1706 removed outlier: 4.070A pdb=" N TYR A1697 " --> pdb=" O GLU A1693 " (cutoff:3.500A) Processing helix chain 'A' and resid 1712 through 1726 Processing helix chain 'A' and resid 1744 through 1763 Processing helix chain 'A' and resid 1788 through 1815 Processing helix chain 'A' and resid 1832 through 1861 removed outlier: 3.614A pdb=" N ALA A1836 " --> pdb=" O GLU A1832 " (cutoff:3.500A) Proline residue: A1846 - end of helix removed outlier: 4.318A pdb=" N ILE A1849 " --> pdb=" O ASN A1845 " (cutoff:3.500A) Processing helix chain 'A' and resid 1882 through 1888 Processing helix chain 'A' and resid 1910 through 1915 removed outlier: 3.674A pdb=" N THR A1915 " --> pdb=" O SER A1911 " (cutoff:3.500A) Processing helix chain 'A' and resid 1923 through 1952 removed outlier: 3.822A pdb=" N CYS A1927 " --> pdb=" O LYS A1923 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A1928 " --> pdb=" O GLU A1924 " (cutoff:3.500A) Proline residue: A1933 - end of helix Proline residue: A1946 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 912 through 914 625 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.12 Time building geometry restraints manager: 2.96 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: 7713 1.04 - 1.25: 1609 1.25 - 1.45: 3697 1.45 - 1.65: 6715 1.65 - 1.86: 111 Bond restraints: 19845 Sorted by residual: bond pdb=" C1 ASG B 8 " pdb=" O5 ASG B 8 " ideal model delta sigma weight residual 1.408 1.509 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C1 ASG B 10 " pdb=" O5 ASG B 10 " ideal model delta sigma weight residual 1.408 1.508 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C1 ASG B 2 " pdb=" O5 ASG B 2 " ideal model delta sigma weight residual 1.408 1.507 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C1 ASG A2701 " pdb=" O5 ASG A2701 " ideal model delta sigma weight residual 1.408 1.507 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C1 BDP B 5 " pdb=" O5 BDP B 5 " ideal model delta sigma weight residual 1.406 1.505 -0.099 2.00e-02 2.50e+03 2.44e+01 ... (remaining 19840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.79: 33971 7.79 - 15.58: 23 15.58 - 23.37: 6 23.37 - 31.17: 6 31.17 - 38.96: 2 Bond angle restraints: 34008 Sorted by residual: angle pdb=" CB VAL A 827 " pdb=" CA VAL A 827 " pdb=" HA VAL A 827 " ideal model delta sigma weight residual 109.00 70.04 38.96 3.00e+00 1.11e-01 1.69e+02 angle pdb=" N VAL A 827 " pdb=" CA VAL A 827 " pdb=" HA VAL A 827 " ideal model delta sigma weight residual 110.00 77.02 32.98 3.00e+00 1.11e-01 1.21e+02 angle pdb=" C VAL A 827 " pdb=" CA VAL A 827 " pdb=" HA VAL A 827 " ideal model delta sigma weight residual 109.00 78.03 30.97 3.00e+00 1.11e-01 1.07e+02 angle pdb=" SD MET A 185 " pdb=" CE MET A 185 " pdb=" HE2 MET A 185 " ideal model delta sigma weight residual 109.00 78.89 30.11 3.00e+00 1.11e-01 1.01e+02 angle pdb=" SD MET A 185 " pdb=" CE MET A 185 " pdb=" HE3 MET A 185 " ideal model delta sigma weight residual 109.00 79.61 29.39 3.00e+00 1.11e-01 9.60e+01 ... (remaining 34003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9149 17.92 - 35.83: 550 35.83 - 53.75: 144 53.75 - 71.66: 30 71.66 - 89.58: 7 Dihedral angle restraints: 9880 sinusoidal: 5118 harmonic: 4762 Sorted by residual: dihedral pdb=" CB CYS A1088 " pdb=" SG CYS A1088 " pdb=" SG CYS A1193 " pdb=" CB CYS A1193 " ideal model delta sinusoidal sigma weight residual -86.00 -160.49 74.49 1 1.00e+01 1.00e-02 7.03e+01 dihedral pdb=" CB CYS A1578 " pdb=" SG CYS A1578 " pdb=" SG CYS A1614 " pdb=" CB CYS A1614 " ideal model delta sinusoidal sigma weight residual 93.00 127.24 -34.24 1 1.00e+01 1.00e-02 1.66e+01 dihedral pdb=" C VAL A 827 " pdb=" N VAL A 827 " pdb=" CA VAL A 827 " pdb=" CB VAL A 827 " ideal model delta harmonic sigma weight residual -122.00 -132.13 10.13 0 2.50e+00 1.60e-01 1.64e+01 ... (remaining 9877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.346: 1698 0.346 - 0.691: 7 0.691 - 1.037: 1 1.037 - 1.383: 0 1.383 - 1.728: 2 Chirality restraints: 1708 Sorted by residual: chirality pdb=" CG LEU A 293 " pdb=" CB LEU A 293 " pdb=" CD1 LEU A 293 " pdb=" CD2 LEU A 293 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.47e+01 chirality pdb=" C3 ASG B 4 " pdb=" C2 ASG B 4 " pdb=" C4 ASG B 4 " pdb=" O3 ASG B 4 " both_signs ideal model delta sigma weight residual False 2.24 0.84 1.40 2.00e-01 2.50e+01 4.87e+01 chirality pdb=" C4 BDP B 3 " pdb=" C3 BDP B 3 " pdb=" C5 BDP B 3 " pdb=" O4 BDP B 3 " both_signs ideal model delta sigma weight residual False -2.49 -1.76 -0.73 2.00e-01 2.50e+01 1.35e+01 ... (remaining 1705 not shown) Planarity restraints: 3104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 942 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO A 943 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 943 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 943 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A1222 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO A1223 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A1223 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1223 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A1787 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO A1788 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A1788 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1788 " 0.020 5.00e-02 4.00e+02 ... (remaining 3101 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 2706 2.31 - 2.88: 36693 2.88 - 3.45: 42158 3.45 - 4.03: 56184 4.03 - 4.60: 87494 Nonbonded interactions: 225235 Sorted by model distance: nonbonded pdb=" H VAL A 827 " pdb=" HA VAL A 827 " model vdw 1.733 1.816 nonbonded pdb="HH22 ARG A1674 " pdb=" O CYS A1777 " model vdw 1.746 2.450 nonbonded pdb=" OD2 ASP A1682 " pdb="HH22 ARG A1792 " model vdw 1.757 2.450 nonbonded pdb="HH22 ARG A1610 " pdb=" OD2 ASP A1688 " model vdw 1.763 2.450 nonbonded pdb=" H TYR A1563 " pdb=" OE1 GLU A1638 " model vdw 1.766 2.450 ... (remaining 225230 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.93 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.780 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6265 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 12156 Z= 0.344 Angle : 1.062 62.353 16373 Z= 0.424 Chirality : 0.075 1.728 1708 Planarity : 0.003 0.038 2056 Dihedral : 11.513 89.581 4536 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.39 % Allowed : 2.47 % Favored : 97.15 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.21), residues: 1363 helix: 1.61 (0.17), residues: 785 sheet: -0.61 (1.81), residues: 10 loop : -2.75 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1674 TYR 0.008 0.001 TYR A1663 PHE 0.010 0.001 PHE A 158 TRP 0.014 0.001 TRP A 663 HIS 0.003 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.33 (12120) covalent geometry : angle 0.82779 / 0.36 (16291) SS BOND : bond 0.00269 / 0.16 ( 26) SS BOND : angle 1.31100 / 0.77 ( 52) hydrogen bonds : bond 0.15338 / 10.15 ( 625) hydrogen bonds : angle 5.10444 / 3.66 ( 1866) link_BETA1-3 : bond 0.07874 / 4.35 ( 5) link_BETA1-3 : angle 3.05900 / 1.45 ( 15) link_BETA1-4 : bond 0.08191 / 4.52 ( 5) link_BETA1-4 : angle 21.70953 / 11.24 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 36 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue VAL 591 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue ILE 617 is missing expected H atoms. Skipping. Residue ILE 618 is missing expected H atoms. Skipping. Residue ALA 619 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue LEU 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LYS 640 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue ILE 678 is missing expected H atoms. Skipping. Residue LEU 719 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 824 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 828 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue TYR 834 is missing expected H atoms. Skipping. Residue TYR 837 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 839 is missing expected H atoms. Skipping. Residue TYR 840 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue ALA 844 is missing expected H atoms. Skipping. Residue LYS 849 is missing expected H atoms. Skipping. Residue ALA 850 is missing expected H atoms. Skipping. Residue THR 852 is missing expected H atoms. Skipping. Residue THR 887 is missing expected H atoms. Skipping. Residue SER 889 is missing expected H atoms. Skipping. Residue SER 890 is missing expected H atoms. Skipping. Residue TYR 891 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 894 is missing expected H atoms. Skipping. Residue VAL 895 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue TYR 972 is missing expected H atoms. Skipping. Residue SER 977 is missing expected H atoms. Skipping. Residue SER 1092 is missing expected H atoms. Skipping. Residue THR 1180 is missing expected H atoms. Skipping. Residue SER 1183 is missing expected H atoms. Skipping. Residue LYS 1185 is missing expected H atoms. Skipping. Residue LEU 1186 is missing expected H atoms. Skipping. Residue ALA 1189 is missing expected H atoms. Skipping. Residue LYS 1191 is missing expected H atoms. Skipping. Residue SER 1198 is missing expected H atoms. Skipping. Residue THR 1199 is missing expected H atoms. Skipping. Residue SER 1213 is missing expected H atoms. Skipping. Residue ILE 1216 is missing expected H atoms. Skipping. Residue ILE 1225 is missing expected H atoms. Skipping. Residue SER 1286 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Residue MET 1318 is missing expected H atoms. Skipping. Residue SER 1331 is missing expected H atoms. Skipping. Residue TYR 1363 is missing expected H atoms. Skipping. Residue LYS 1422 is missing expected H atoms. Skipping. Residue THR 1425 is missing expected H atoms. Skipping. Residue SER 1427 is missing expected H atoms. Skipping. Residue ILE 1433 is missing expected H atoms. Skipping. Residue LYS 1464 is missing expected H atoms. Skipping. Residue LYS 1626 is missing expected H atoms. Skipping. Residue ILE 1629 is missing expected H atoms. Skipping. Residue THR 1630 is missing expected H atoms. Skipping. Residue LYS 1634 is missing expected H atoms. Skipping. Residue ALA 1657 is missing expected H atoms. Skipping. Residue TYR 1663 is missing expected H atoms. Skipping. Residue LEU 1664 is missing expected H atoms. Skipping. Residue LYS 1711 is missing expected H atoms. Skipping. Residue LYS 1759 is missing expected H atoms. Skipping. Residue ILE 1761 is missing expected H atoms. Skipping. Residue THR 1841 is missing expected H atoms. Skipping. Residue TYR 1862 is missing expected H atoms. Skipping. Residue SER 1911 is missing expected H atoms. Skipping. Residue LYS 1939 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1758 ARG cc_start: 0.7042 (mtp85) cc_final: 0.6673 (mtp85) outliers start: 5 outliers final: 0 residues processed: 107 average time/residue: 0.1927 time to fit residues: 31.0206 Evaluate side-chains 70 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.0970 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 ASN A1573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.234829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.213957 restraints weight = 30355.796| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 1.75 r_work: 0.4194 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4236 r_free = 0.4236 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4233 r_free = 0.4233 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.4233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12156 Z= 0.134 Angle : 0.532 9.797 16373 Z= 0.269 Chirality : 0.055 1.689 1708 Planarity : 0.003 0.034 2056 Dihedral : 3.821 51.408 1530 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.69 % Allowed : 5.09 % Favored : 94.22 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.24), residues: 1363 helix: 2.39 (0.18), residues: 813 sheet: -0.69 (1.81), residues: 10 loop : -2.62 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1792 TYR 0.016 0.001 TYR A1649 PHE 0.010 0.001 PHE A 650 TRP 0.010 0.001 TRP A 718 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (12120) covalent geometry : angle 0.50740 / 0.26 (16291) SS BOND : bond 0.00244 / 0.16 ( 26) SS BOND : angle 1.86309 / 0.99 ( 52) hydrogen bonds : bond 0.04221 / 2.92 ( 625) hydrogen bonds : angle 3.57803 / 2.55 ( 1866) link_BETA1-3 : bond 0.00673 / 0.36 ( 5) link_BETA1-3 : angle 1.05146 / 0.57 ( 15) link_BETA1-4 : bond 0.00806 / 0.41 ( 5) link_BETA1-4 : angle 3.98921 / 2.02 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 36 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue VAL 591 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue ILE 617 is missing expected H atoms. Skipping. Residue ILE 618 is missing expected H atoms. Skipping. Residue ALA 619 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue LEU 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LYS 640 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue ILE 678 is missing expected H atoms. Skipping. Residue LEU 719 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 824 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 828 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue TYR 834 is missing expected H atoms. Skipping. Residue TYR 837 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 839 is missing expected H atoms. Skipping. Residue TYR 840 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue ALA 844 is missing expected H atoms. Skipping. Residue LYS 849 is missing expected H atoms. Skipping. Residue ALA 850 is missing expected H atoms. Skipping. Residue THR 852 is missing expected H atoms. Skipping. Residue THR 887 is missing expected H atoms. Skipping. Residue SER 889 is missing expected H atoms. Skipping. Residue SER 890 is missing expected H atoms. Skipping. Residue TYR 891 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 894 is missing expected H atoms. Skipping. Residue VAL 895 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue TYR 972 is missing expected H atoms. Skipping. Residue SER 977 is missing expected H atoms. Skipping. Residue SER 1092 is missing expected H atoms. Skipping. Residue THR 1180 is missing expected H atoms. Skipping. Residue SER 1183 is missing expected H atoms. Skipping. Residue LYS 1185 is missing expected H atoms. Skipping. Residue LEU 1186 is missing expected H atoms. Skipping. Residue ALA 1189 is missing expected H atoms. Skipping. Residue LYS 1191 is missing expected H atoms. Skipping. Residue SER 1198 is missing expected H atoms. Skipping. Residue THR 1199 is missing expected H atoms. Skipping. Residue SER 1213 is missing expected H atoms. Skipping. Residue ILE 1216 is missing expected H atoms. Skipping. Residue ILE 1225 is missing expected H atoms. Skipping. Residue SER 1286 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Residue MET 1318 is missing expected H atoms. Skipping. Residue SER 1331 is missing expected H atoms. Skipping. Residue TYR 1363 is missing expected H atoms. Skipping. Residue LYS 1422 is missing expected H atoms. Skipping. Residue THR 1425 is missing expected H atoms. Skipping. Residue SER 1427 is missing expected H atoms. Skipping. Residue ILE 1433 is missing expected H atoms. Skipping. Residue LYS 1464 is missing expected H atoms. Skipping. Residue LYS 1626 is missing expected H atoms. Skipping. Residue ILE 1629 is missing expected H atoms. Skipping. Residue THR 1630 is missing expected H atoms. Skipping. Residue LYS 1634 is missing expected H atoms. Skipping. Residue ALA 1657 is missing expected H atoms. Skipping. Residue TYR 1663 is missing expected H atoms. Skipping. Residue LEU 1664 is missing expected H atoms. Skipping. Residue LYS 1711 is missing expected H atoms. Skipping. Residue LYS 1759 is missing expected H atoms. Skipping. Residue ILE 1761 is missing expected H atoms. Skipping. Residue THR 1841 is missing expected H atoms. Skipping. Residue TYR 1862 is missing expected H atoms. Skipping. Residue SER 1911 is missing expected H atoms. Skipping. Residue LYS 1939 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.4715 (m-30) cc_final: 0.4430 (m-30) REVERT: A 716 TYR cc_start: 0.6755 (m-80) cc_final: 0.6241 (m-80) REVERT: A 721 MET cc_start: 0.6596 (OUTLIER) cc_final: 0.6228 (mtm) REVERT: A 993 TYR cc_start: 0.4632 (m-10) cc_final: 0.3201 (p90) REVERT: A 1578 CYS cc_start: 0.4470 (m) cc_final: 0.4175 (m) outliers start: 9 outliers final: 7 residues processed: 95 average time/residue: 0.1701 time to fit residues: 25.4639 Evaluate side-chains 86 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1812 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 41 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 141 optimal weight: 0.0970 chunk 26 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 571 GLN ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 ASN A 946 ASN A1538 ASN A1641 GLN A1942 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.226036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.216492 restraints weight = 30214.130| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 0.58 r_work: 0.4199 rms_B_bonded: 1.12 restraints_weight: 0.5000 r_work: 0.4091 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4042 r_free = 0.4042 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4042 r_free = 0.4042 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.4042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12156 Z= 0.112 Angle : 0.472 10.100 16373 Z= 0.243 Chirality : 0.054 1.695 1708 Planarity : 0.003 0.033 2056 Dihedral : 3.796 57.105 1530 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.16 % Allowed : 6.09 % Favored : 92.75 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.24), residues: 1363 helix: 2.63 (0.18), residues: 814 sheet: 0.21 (2.04), residues: 10 loop : -2.59 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 230 TYR 0.015 0.001 TYR A1305 PHE 0.012 0.001 PHE A 683 TRP 0.010 0.001 TRP A 213 HIS 0.003 0.001 HIS A 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (12120) covalent geometry : angle 0.45732 / 0.24 (16291) SS BOND : bond 0.00243 / 0.16 ( 26) SS BOND : angle 1.43949 / 0.80 ( 52) hydrogen bonds : bond 0.04102 / 2.86 ( 625) hydrogen bonds : angle 3.37978 / 2.41 ( 1866) link_BETA1-3 : bond 0.00258 / 0.14 ( 5) link_BETA1-3 : angle 1.30185 / 0.70 ( 15) link_BETA1-4 : bond 0.00415 / 0.22 ( 5) link_BETA1-4 : angle 2.71545 / 1.38 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 36 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue VAL 591 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue ILE 617 is missing expected H atoms. Skipping. Residue ILE 618 is missing expected H atoms. Skipping. Residue ALA 619 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue LEU 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LYS 640 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue ILE 678 is missing expected H atoms. Skipping. Residue LEU 719 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 824 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 828 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue TYR 834 is missing expected H atoms. Skipping. Residue TYR 837 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 839 is missing expected H atoms. Skipping. Residue TYR 840 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue ALA 844 is missing expected H atoms. Skipping. Residue LYS 849 is missing expected H atoms. Skipping. Residue ALA 850 is missing expected H atoms. Skipping. Residue THR 852 is missing expected H atoms. Skipping. Residue THR 887 is missing expected H atoms. Skipping. Residue SER 889 is missing expected H atoms. Skipping. Residue SER 890 is missing expected H atoms. Skipping. Residue TYR 891 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 894 is missing expected H atoms. Skipping. Residue VAL 895 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue TYR 972 is missing expected H atoms. Skipping. Residue SER 977 is missing expected H atoms. Skipping. Residue SER 1092 is missing expected H atoms. Skipping. Residue THR 1180 is missing expected H atoms. Skipping. Residue SER 1183 is missing expected H atoms. Skipping. Residue LYS 1185 is missing expected H atoms. Skipping. Residue LEU 1186 is missing expected H atoms. Skipping. Residue ALA 1189 is missing expected H atoms. Skipping. Residue LYS 1191 is missing expected H atoms. Skipping. Residue SER 1198 is missing expected H atoms. Skipping. Residue THR 1199 is missing expected H atoms. Skipping. Residue SER 1213 is missing expected H atoms. Skipping. Residue ILE 1216 is missing expected H atoms. Skipping. Residue ILE 1225 is missing expected H atoms. Skipping. Residue SER 1286 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Residue MET 1318 is missing expected H atoms. Skipping. Residue SER 1331 is missing expected H atoms. Skipping. Residue TYR 1363 is missing expected H atoms. Skipping. Residue LYS 1422 is missing expected H atoms. Skipping. Residue THR 1425 is missing expected H atoms. Skipping. Residue SER 1427 is missing expected H atoms. Skipping. Residue ILE 1433 is missing expected H atoms. Skipping. Residue LYS 1464 is missing expected H atoms. Skipping. Residue LYS 1626 is missing expected H atoms. Skipping. Residue ILE 1629 is missing expected H atoms. Skipping. Residue THR 1630 is missing expected H atoms. Skipping. Residue LYS 1634 is missing expected H atoms. Skipping. Residue ALA 1657 is missing expected H atoms. Skipping. Residue TYR 1663 is missing expected H atoms. Skipping. Residue LEU 1664 is missing expected H atoms. Skipping. Residue LYS 1711 is missing expected H atoms. Skipping. Residue LYS 1759 is missing expected H atoms. Skipping. Residue ILE 1761 is missing expected H atoms. Skipping. Residue THR 1841 is missing expected H atoms. Skipping. Residue TYR 1862 is missing expected H atoms. Skipping. Residue SER 1911 is missing expected H atoms. Skipping. Residue LYS 1939 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.5105 (m-30) cc_final: 0.4811 (m-30) REVERT: A 716 TYR cc_start: 0.6834 (m-80) cc_final: 0.6111 (m-80) REVERT: A 721 MET cc_start: 0.6737 (OUTLIER) cc_final: 0.6436 (mtm) REVERT: A 993 TYR cc_start: 0.4760 (m-10) cc_final: 0.2409 (p90) REVERT: A 1578 CYS cc_start: 0.4762 (m) cc_final: 0.4454 (m) REVERT: A 1887 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7639 (mm) outliers start: 15 outliers final: 7 residues processed: 98 average time/residue: 0.1607 time to fit residues: 25.0284 Evaluate side-chains 94 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 900 ILE Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1088 CYS Chi-restraints excluded: chain A residue 1140 CYS Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1887 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 81 optimal weight: 0.0970 chunk 10 optimal weight: 0.0670 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 125 optimal weight: 0.6980 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1839 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.222914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.214384 restraints weight = 30384.863| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 0.48 r_work: 0.4218 rms_B_bonded: 0.78 restraints_weight: 0.5000 r_work: 0.4106 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4052 r_free = 0.4052 target_work(ls_wunit_k1) = 0.189 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4052 r_free = 0.4052 target_work(ls_wunit_k1) = 0.189 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.4052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12156 Z= 0.099 Angle : 0.448 10.030 16373 Z= 0.231 Chirality : 0.054 1.696 1708 Planarity : 0.003 0.031 2056 Dihedral : 3.695 58.099 1530 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.23 % Allowed : 6.55 % Favored : 92.21 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.24), residues: 1363 helix: 2.78 (0.18), residues: 817 sheet: 0.32 (2.09), residues: 10 loop : -2.57 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 230 TYR 0.014 0.001 TYR A1305 PHE 0.009 0.001 PHE A 650 TRP 0.011 0.001 TRP A 213 HIS 0.003 0.001 HIS A 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (12120) covalent geometry : angle 0.43669 / 0.23 (16291) SS BOND : bond 0.00241 / 0.15 ( 26) SS BOND : angle 1.33286 / 0.73 ( 52) hydrogen bonds : bond 0.03667 / 2.59 ( 625) hydrogen bonds : angle 3.20492 / 2.27 ( 1866) link_BETA1-3 : bond 0.00306 / 0.16 ( 5) link_BETA1-3 : angle 1.00261 / 0.53 ( 15) link_BETA1-4 : bond 0.00448 / 0.23 ( 5) link_BETA1-4 : angle 2.08437 / 1.03 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 36 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue VAL 591 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue ILE 617 is missing expected H atoms. Skipping. Residue ILE 618 is missing expected H atoms. Skipping. Residue ALA 619 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue LEU 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LYS 640 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue ILE 678 is missing expected H atoms. Skipping. Residue LEU 719 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 824 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 828 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue TYR 834 is missing expected H atoms. Skipping. Residue TYR 837 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 839 is missing expected H atoms. Skipping. Residue TYR 840 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue ALA 844 is missing expected H atoms. Skipping. Residue LYS 849 is missing expected H atoms. Skipping. Residue ALA 850 is missing expected H atoms. Skipping. Residue THR 852 is missing expected H atoms. Skipping. Residue THR 887 is missing expected H atoms. Skipping. Residue SER 889 is missing expected H atoms. Skipping. Residue SER 890 is missing expected H atoms. Skipping. Residue TYR 891 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 894 is missing expected H atoms. Skipping. Residue VAL 895 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue TYR 972 is missing expected H atoms. Skipping. Residue SER 977 is missing expected H atoms. Skipping. Residue SER 1092 is missing expected H atoms. Skipping. Residue THR 1180 is missing expected H atoms. Skipping. Residue SER 1183 is missing expected H atoms. Skipping. Residue LYS 1185 is missing expected H atoms. Skipping. Residue LEU 1186 is missing expected H atoms. Skipping. Residue ALA 1189 is missing expected H atoms. Skipping. Residue LYS 1191 is missing expected H atoms. Skipping. Residue SER 1198 is missing expected H atoms. Skipping. Residue THR 1199 is missing expected H atoms. Skipping. Residue SER 1213 is missing expected H atoms. Skipping. Residue ILE 1216 is missing expected H atoms. Skipping. Residue ILE 1225 is missing expected H atoms. Skipping. Residue SER 1286 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Residue MET 1318 is missing expected H atoms. Skipping. Residue SER 1331 is missing expected H atoms. Skipping. Residue TYR 1363 is missing expected H atoms. Skipping. Residue LYS 1422 is missing expected H atoms. Skipping. Residue THR 1425 is missing expected H atoms. Skipping. Residue SER 1427 is missing expected H atoms. Skipping. Residue ILE 1433 is missing expected H atoms. Skipping. Residue LYS 1464 is missing expected H atoms. Skipping. Residue LYS 1626 is missing expected H atoms. Skipping. Residue ILE 1629 is missing expected H atoms. Skipping. Residue THR 1630 is missing expected H atoms. Skipping. Residue LYS 1634 is missing expected H atoms. Skipping. Residue ALA 1657 is missing expected H atoms. Skipping. Residue TYR 1663 is missing expected H atoms. Skipping. Residue LEU 1664 is missing expected H atoms. Skipping. Residue LYS 1711 is missing expected H atoms. Skipping. Residue LYS 1759 is missing expected H atoms. Skipping. Residue ILE 1761 is missing expected H atoms. Skipping. Residue THR 1841 is missing expected H atoms. Skipping. Residue TYR 1862 is missing expected H atoms. Skipping. Residue SER 1911 is missing expected H atoms. Skipping. Residue LYS 1939 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 716 TYR cc_start: 0.6978 (m-80) cc_final: 0.6192 (m-80) REVERT: A 721 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6551 (mtm) REVERT: A 1578 CYS cc_start: 0.5058 (m) cc_final: 0.4777 (m) outliers start: 16 outliers final: 11 residues processed: 96 average time/residue: 0.1625 time to fit residues: 24.4828 Evaluate side-chains 96 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1088 CYS Chi-restraints excluded: chain A residue 1140 CYS Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1345 SER Chi-restraints excluded: chain A residue 1812 MET Chi-restraints excluded: chain A residue 1887 LEU Chi-restraints excluded: chain A residue 1944 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 117 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 2 optimal weight: 0.0870 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 0.0170 chunk 90 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 125 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 HIS ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1150 ASN A1261 GLN A1443 GLN A1504 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.215302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.201333 restraints weight = 30035.418| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 0.86 r_work: 0.4067 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3940 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3892 r_free = 0.3892 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3892 r_free = 0.3892 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12156 Z= 0.124 Angle : 0.485 10.026 16373 Z= 0.253 Chirality : 0.054 1.698 1708 Planarity : 0.003 0.035 2056 Dihedral : 3.765 57.103 1530 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.93 % Allowed : 6.94 % Favored : 92.14 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.24), residues: 1363 helix: 2.66 (0.18), residues: 823 sheet: 0.06 (1.97), residues: 10 loop : -2.55 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 230 TYR 0.016 0.001 TYR A1305 PHE 0.011 0.001 PHE A 650 TRP 0.014 0.001 TRP A 213 HIS 0.004 0.001 HIS A1666 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (12120) covalent geometry : angle 0.47222 / 0.25 (16291) SS BOND : bond 0.00465 / 0.25 ( 26) SS BOND : angle 1.55358 / 0.85 ( 52) hydrogen bonds : bond 0.04043 / 2.85 ( 625) hydrogen bonds : angle 3.27172 / 2.33 ( 1866) link_BETA1-3 : bond 0.00162 / 0.08 ( 5) link_BETA1-3 : angle 1.19180 / 0.64 ( 15) link_BETA1-4 : bond 0.00502 / 0.26 ( 5) link_BETA1-4 : angle 2.24023 / 1.12 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 36 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue VAL 591 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue ILE 617 is missing expected H atoms. Skipping. Residue ILE 618 is missing expected H atoms. Skipping. Residue ALA 619 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue LEU 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LYS 640 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue ILE 678 is missing expected H atoms. Skipping. Residue LEU 719 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 824 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 828 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue TYR 834 is missing expected H atoms. Skipping. Residue TYR 837 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 839 is missing expected H atoms. Skipping. Residue TYR 840 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue ALA 844 is missing expected H atoms. Skipping. Residue LYS 849 is missing expected H atoms. Skipping. Residue ALA 850 is missing expected H atoms. Skipping. Residue THR 852 is missing expected H atoms. Skipping. Residue THR 887 is missing expected H atoms. Skipping. Residue SER 889 is missing expected H atoms. Skipping. Residue SER 890 is missing expected H atoms. Skipping. Residue TYR 891 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 894 is missing expected H atoms. Skipping. Residue VAL 895 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue TYR 972 is missing expected H atoms. Skipping. Residue SER 977 is missing expected H atoms. Skipping. Residue SER 1092 is missing expected H atoms. Skipping. Residue THR 1180 is missing expected H atoms. Skipping. Residue SER 1183 is missing expected H atoms. Skipping. Residue LYS 1185 is missing expected H atoms. Skipping. Residue LEU 1186 is missing expected H atoms. Skipping. Residue ALA 1189 is missing expected H atoms. Skipping. Residue LYS 1191 is missing expected H atoms. Skipping. Residue SER 1198 is missing expected H atoms. Skipping. Residue THR 1199 is missing expected H atoms. Skipping. Residue SER 1213 is missing expected H atoms. Skipping. Residue ILE 1216 is missing expected H atoms. Skipping. Residue ILE 1225 is missing expected H atoms. Skipping. Residue SER 1286 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Residue MET 1318 is missing expected H atoms. Skipping. Residue SER 1331 is missing expected H atoms. Skipping. Residue TYR 1363 is missing expected H atoms. Skipping. Residue LYS 1422 is missing expected H atoms. Skipping. Residue THR 1425 is missing expected H atoms. Skipping. Residue SER 1427 is missing expected H atoms. Skipping. Residue ILE 1433 is missing expected H atoms. Skipping. Residue LYS 1464 is missing expected H atoms. Skipping. Residue LYS 1626 is missing expected H atoms. Skipping. Residue ILE 1629 is missing expected H atoms. Skipping. Residue THR 1630 is missing expected H atoms. Skipping. Residue LYS 1634 is missing expected H atoms. Skipping. Residue ALA 1657 is missing expected H atoms. Skipping. Residue TYR 1663 is missing expected H atoms. Skipping. Residue LEU 1664 is missing expected H atoms. Skipping. Residue LYS 1711 is missing expected H atoms. Skipping. Residue LYS 1759 is missing expected H atoms. Skipping. Residue ILE 1761 is missing expected H atoms. Skipping. Residue THR 1841 is missing expected H atoms. Skipping. Residue TYR 1862 is missing expected H atoms. Skipping. Residue SER 1911 is missing expected H atoms. Skipping. Residue LYS 1939 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 716 TYR cc_start: 0.7332 (m-80) cc_final: 0.6459 (m-80) REVERT: A 1147 LYS cc_start: 0.8634 (tppp) cc_final: 0.8424 (tppt) REVERT: A 1785 ILE cc_start: 0.9079 (pt) cc_final: 0.8834 (tt) outliers start: 12 outliers final: 9 residues processed: 101 average time/residue: 0.1889 time to fit residues: 28.5617 Evaluate side-chains 94 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1088 CYS Chi-restraints excluded: chain A residue 1140 CYS Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1887 LEU Chi-restraints excluded: chain A residue 1944 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 51 optimal weight: 0.0050 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 ASN ** A1666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.223233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.214153 restraints weight = 30137.042| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 0.56 r_work: 0.4132 rms_B_bonded: 0.88 restraints_weight: 0.5000 r_work: 0.4020 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3992 r_free = 0.3992 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3992 r_free = 0.3992 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12156 Z= 0.153 Angle : 0.522 9.932 16373 Z= 0.278 Chirality : 0.055 1.695 1708 Planarity : 0.003 0.045 2056 Dihedral : 4.017 53.741 1530 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.46 % Allowed : 7.32 % Favored : 91.21 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.24), residues: 1363 helix: 2.49 (0.18), residues: 816 sheet: 0.11 (2.04), residues: 10 loop : -2.63 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 132 TYR 0.021 0.002 TYR A 574 PHE 0.012 0.001 PHE A 650 TRP 0.018 0.001 TRP A 213 HIS 0.004 0.001 HIS A1666 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (12120) covalent geometry : angle 0.51046 / 0.27 (16291) SS BOND : bond 0.00345 / 0.22 ( 26) SS BOND : angle 1.55123 / 0.85 ( 52) hydrogen bonds : bond 0.04394 / 3.11 ( 625) hydrogen bonds : angle 3.41594 / 2.43 ( 1866) link_BETA1-3 : bond 0.00201 / 0.12 ( 5) link_BETA1-3 : angle 1.14006 / 0.61 ( 15) link_BETA1-4 : bond 0.00340 / 0.17 ( 5) link_BETA1-4 : angle 2.19079 / 1.08 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 36 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue VAL 591 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue ILE 617 is missing expected H atoms. Skipping. Residue ILE 618 is missing expected H atoms. Skipping. Residue ALA 619 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue LEU 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LYS 640 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue ILE 678 is missing expected H atoms. Skipping. Residue LEU 719 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 824 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 828 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue TYR 834 is missing expected H atoms. Skipping. Residue TYR 837 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 839 is missing expected H atoms. Skipping. Residue TYR 840 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue ALA 844 is missing expected H atoms. Skipping. Residue LYS 849 is missing expected H atoms. Skipping. Residue ALA 850 is missing expected H atoms. Skipping. Residue THR 852 is missing expected H atoms. Skipping. Residue THR 887 is missing expected H atoms. Skipping. Residue SER 889 is missing expected H atoms. Skipping. Residue SER 890 is missing expected H atoms. Skipping. Residue TYR 891 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 894 is missing expected H atoms. Skipping. Residue VAL 895 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue TYR 972 is missing expected H atoms. Skipping. Residue SER 977 is missing expected H atoms. Skipping. Residue SER 1092 is missing expected H atoms. Skipping. Residue THR 1180 is missing expected H atoms. Skipping. Residue SER 1183 is missing expected H atoms. Skipping. Residue LYS 1185 is missing expected H atoms. Skipping. Residue LEU 1186 is missing expected H atoms. Skipping. Residue ALA 1189 is missing expected H atoms. Skipping. Residue LYS 1191 is missing expected H atoms. Skipping. Residue SER 1198 is missing expected H atoms. Skipping. Residue THR 1199 is missing expected H atoms. Skipping. Residue SER 1213 is missing expected H atoms. Skipping. Residue ILE 1216 is missing expected H atoms. Skipping. Residue ILE 1225 is missing expected H atoms. Skipping. Residue SER 1286 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Residue MET 1318 is missing expected H atoms. Skipping. Residue SER 1331 is missing expected H atoms. Skipping. Residue TYR 1363 is missing expected H atoms. Skipping. Residue LYS 1422 is missing expected H atoms. Skipping. Residue THR 1425 is missing expected H atoms. Skipping. Residue SER 1427 is missing expected H atoms. Skipping. Residue ILE 1433 is missing expected H atoms. Skipping. Residue LYS 1464 is missing expected H atoms. Skipping. Residue LYS 1626 is missing expected H atoms. Skipping. Residue ILE 1629 is missing expected H atoms. Skipping. Residue THR 1630 is missing expected H atoms. Skipping. Residue LYS 1634 is missing expected H atoms. Skipping. Residue ALA 1657 is missing expected H atoms. Skipping. Residue TYR 1663 is missing expected H atoms. Skipping. Residue LEU 1664 is missing expected H atoms. Skipping. Residue LYS 1711 is missing expected H atoms. Skipping. Residue LYS 1759 is missing expected H atoms. Skipping. Residue ILE 1761 is missing expected H atoms. Skipping. Residue THR 1841 is missing expected H atoms. Skipping. Residue TYR 1862 is missing expected H atoms. Skipping. Residue SER 1911 is missing expected H atoms. Skipping. Residue LYS 1939 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 716 TYR cc_start: 0.7366 (m-80) cc_final: 0.6464 (m-80) REVERT: A 840 TYR cc_start: 0.7288 (m-10) cc_final: 0.6995 (m-10) REVERT: A 993 TYR cc_start: 0.7016 (m-80) cc_final: 0.3735 (t80) REVERT: A 1147 LYS cc_start: 0.8629 (tppp) cc_final: 0.8425 (tppt) REVERT: A 1349 TYR cc_start: 0.7530 (m-80) cc_final: 0.6927 (m-80) REVERT: A 1785 ILE cc_start: 0.9031 (pt) cc_final: 0.8793 (tt) outliers start: 19 outliers final: 15 residues processed: 103 average time/residue: 0.1797 time to fit residues: 28.4585 Evaluate side-chains 102 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1088 CYS Chi-restraints excluded: chain A residue 1140 CYS Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1168 ILE Chi-restraints excluded: chain A residue 1463 GLU Chi-restraints excluded: chain A residue 1887 LEU Chi-restraints excluded: chain A residue 1944 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 110 optimal weight: 0.3980 chunk 27 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.217227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.196222 restraints weight = 30468.378| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 1.60 r_work: 0.4019 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3905 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3949 r_free = 0.3949 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3949 r_free = 0.3949 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12156 Z= 0.116 Angle : 0.476 9.965 16373 Z= 0.251 Chirality : 0.054 1.698 1708 Planarity : 0.003 0.038 2056 Dihedral : 3.907 55.110 1530 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.23 % Allowed : 8.25 % Favored : 90.52 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.24), residues: 1363 helix: 2.56 (0.18), residues: 820 sheet: 0.13 (2.04), residues: 10 loop : -2.59 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 132 TYR 0.015 0.001 TYR A1305 PHE 0.011 0.001 PHE A 650 TRP 0.016 0.001 TRP A 213 HIS 0.003 0.001 HIS A1666 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (12120) covalent geometry : angle 0.46624 / 0.25 (16291) SS BOND : bond 0.00276 / 0.18 ( 26) SS BOND : angle 1.34298 / 0.74 ( 52) hydrogen bonds : bond 0.04136 / 2.92 ( 625) hydrogen bonds : angle 3.35368 / 2.39 ( 1866) link_BETA1-3 : bond 0.00174 / 0.10 ( 5) link_BETA1-3 : angle 1.10895 / 0.61 ( 15) link_BETA1-4 : bond 0.00382 / 0.20 ( 5) link_BETA1-4 : angle 2.03138 / 1.00 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 36 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue VAL 591 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue ILE 617 is missing expected H atoms. Skipping. Residue ILE 618 is missing expected H atoms. Skipping. Residue ALA 619 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue LEU 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LYS 640 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue ILE 678 is missing expected H atoms. Skipping. Residue LEU 719 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 824 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 828 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue TYR 834 is missing expected H atoms. Skipping. Residue TYR 837 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 839 is missing expected H atoms. Skipping. Residue TYR 840 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue ALA 844 is missing expected H atoms. Skipping. Residue LYS 849 is missing expected H atoms. Skipping. Residue ALA 850 is missing expected H atoms. Skipping. Residue THR 852 is missing expected H atoms. Skipping. Residue THR 887 is missing expected H atoms. Skipping. Residue SER 889 is missing expected H atoms. Skipping. Residue SER 890 is missing expected H atoms. Skipping. Residue TYR 891 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 894 is missing expected H atoms. Skipping. Residue VAL 895 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue TYR 972 is missing expected H atoms. Skipping. Residue SER 977 is missing expected H atoms. Skipping. Residue SER 1092 is missing expected H atoms. Skipping. Residue THR 1180 is missing expected H atoms. Skipping. Residue SER 1183 is missing expected H atoms. Skipping. Residue LYS 1185 is missing expected H atoms. Skipping. Residue LEU 1186 is missing expected H atoms. Skipping. Residue ALA 1189 is missing expected H atoms. Skipping. Residue LYS 1191 is missing expected H atoms. Skipping. Residue SER 1198 is missing expected H atoms. Skipping. Residue THR 1199 is missing expected H atoms. Skipping. Residue SER 1213 is missing expected H atoms. Skipping. Residue ILE 1216 is missing expected H atoms. Skipping. Residue ILE 1225 is missing expected H atoms. Skipping. Residue SER 1286 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Residue MET 1318 is missing expected H atoms. Skipping. Residue SER 1331 is missing expected H atoms. Skipping. Residue TYR 1363 is missing expected H atoms. Skipping. Residue LYS 1422 is missing expected H atoms. Skipping. Residue THR 1425 is missing expected H atoms. Skipping. Residue SER 1427 is missing expected H atoms. Skipping. Residue ILE 1433 is missing expected H atoms. Skipping. Residue LYS 1464 is missing expected H atoms. Skipping. Residue LYS 1626 is missing expected H atoms. Skipping. Residue ILE 1629 is missing expected H atoms. Skipping. Residue THR 1630 is missing expected H atoms. Skipping. Residue LYS 1634 is missing expected H atoms. Skipping. Residue ALA 1657 is missing expected H atoms. Skipping. Residue TYR 1663 is missing expected H atoms. Skipping. Residue LEU 1664 is missing expected H atoms. Skipping. Residue LYS 1711 is missing expected H atoms. Skipping. Residue LYS 1759 is missing expected H atoms. Skipping. Residue ILE 1761 is missing expected H atoms. Skipping. Residue THR 1841 is missing expected H atoms. Skipping. Residue TYR 1862 is missing expected H atoms. Skipping. Residue SER 1911 is missing expected H atoms. Skipping. Residue LYS 1939 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7558 (tpt170) cc_final: 0.7165 (tpt170) REVERT: A 573 GLU cc_start: 0.7947 (tp30) cc_final: 0.7707 (tp30) REVERT: A 716 TYR cc_start: 0.7679 (m-80) cc_final: 0.6770 (m-80) REVERT: A 840 TYR cc_start: 0.7493 (m-10) cc_final: 0.7186 (m-10) REVERT: A 993 TYR cc_start: 0.7214 (m-80) cc_final: 0.3572 (t80) REVERT: A 1349 TYR cc_start: 0.7658 (m-80) cc_final: 0.7114 (m-80) outliers start: 16 outliers final: 13 residues processed: 94 average time/residue: 0.1734 time to fit residues: 24.9227 Evaluate side-chains 98 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1088 CYS Chi-restraints excluded: chain A residue 1140 CYS Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1887 LEU Chi-restraints excluded: chain A residue 1937 MET Chi-restraints excluded: chain A residue 1944 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 61 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1524 ASN ** A1666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.213363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.192058 restraints weight = 30655.032| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 1.36 r_work: 0.3922 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3904 r_free = 0.3904 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3904 r_free = 0.3904 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12156 Z= 0.133 Angle : 0.494 9.942 16373 Z= 0.263 Chirality : 0.055 1.699 1708 Planarity : 0.003 0.040 2056 Dihedral : 3.967 55.349 1530 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 1.23 % Allowed : 8.40 % Favored : 90.36 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.24), residues: 1363 helix: 2.51 (0.18), residues: 818 sheet: -0.02 (2.01), residues: 10 loop : -2.60 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 132 TYR 0.014 0.001 TYR A1305 PHE 0.012 0.001 PHE A 650 TRP 0.018 0.001 TRP A 213 HIS 0.003 0.001 HIS A1666 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (12120) covalent geometry : angle 0.48365 / 0.26 (16291) SS BOND : bond 0.00304 / 0.20 ( 26) SS BOND : angle 1.39677 / 0.78 ( 52) hydrogen bonds : bond 0.04199 / 2.96 ( 625) hydrogen bonds : angle 3.39639 / 2.42 ( 1866) link_BETA1-3 : bond 0.00214 / 0.12 ( 5) link_BETA1-3 : angle 1.13039 / 0.62 ( 15) link_BETA1-4 : bond 0.00348 / 0.18 ( 5) link_BETA1-4 : angle 2.00495 / 0.98 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 36 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue VAL 591 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue ILE 617 is missing expected H atoms. Skipping. Residue ILE 618 is missing expected H atoms. Skipping. Residue ALA 619 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue LEU 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LYS 640 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue ILE 678 is missing expected H atoms. Skipping. Residue LEU 719 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 824 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 828 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue TYR 834 is missing expected H atoms. Skipping. Residue TYR 837 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 839 is missing expected H atoms. Skipping. Residue TYR 840 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue ALA 844 is missing expected H atoms. Skipping. Residue LYS 849 is missing expected H atoms. Skipping. Residue ALA 850 is missing expected H atoms. Skipping. Residue THR 852 is missing expected H atoms. Skipping. Residue THR 887 is missing expected H atoms. Skipping. Residue SER 889 is missing expected H atoms. Skipping. Residue SER 890 is missing expected H atoms. Skipping. Residue TYR 891 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 894 is missing expected H atoms. Skipping. Residue VAL 895 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue TYR 972 is missing expected H atoms. Skipping. Residue SER 977 is missing expected H atoms. Skipping. Residue SER 1092 is missing expected H atoms. Skipping. Residue THR 1180 is missing expected H atoms. Skipping. Residue SER 1183 is missing expected H atoms. Skipping. Residue LYS 1185 is missing expected H atoms. Skipping. Residue LEU 1186 is missing expected H atoms. Skipping. Residue ALA 1189 is missing expected H atoms. Skipping. Residue LYS 1191 is missing expected H atoms. Skipping. Residue SER 1198 is missing expected H atoms. Skipping. Residue THR 1199 is missing expected H atoms. Skipping. Residue SER 1213 is missing expected H atoms. Skipping. Residue ILE 1216 is missing expected H atoms. Skipping. Residue ILE 1225 is missing expected H atoms. Skipping. Residue SER 1286 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Residue MET 1318 is missing expected H atoms. Skipping. Residue SER 1331 is missing expected H atoms. Skipping. Residue TYR 1363 is missing expected H atoms. Skipping. Residue LYS 1422 is missing expected H atoms. Skipping. Residue THR 1425 is missing expected H atoms. Skipping. Residue SER 1427 is missing expected H atoms. Skipping. Residue ILE 1433 is missing expected H atoms. Skipping. Residue LYS 1464 is missing expected H atoms. Skipping. Residue LYS 1626 is missing expected H atoms. Skipping. Residue ILE 1629 is missing expected H atoms. Skipping. Residue THR 1630 is missing expected H atoms. Skipping. Residue LYS 1634 is missing expected H atoms. Skipping. Residue ALA 1657 is missing expected H atoms. Skipping. Residue TYR 1663 is missing expected H atoms. Skipping. Residue LEU 1664 is missing expected H atoms. Skipping. Residue LYS 1711 is missing expected H atoms. Skipping. Residue LYS 1759 is missing expected H atoms. Skipping. Residue ILE 1761 is missing expected H atoms. Skipping. Residue THR 1841 is missing expected H atoms. Skipping. Residue TYR 1862 is missing expected H atoms. Skipping. Residue SER 1911 is missing expected H atoms. Skipping. Residue LYS 1939 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7708 (tpt170) cc_final: 0.7452 (tpt170) REVERT: A 212 ASP cc_start: 0.1707 (OUTLIER) cc_final: 0.0407 (t0) REVERT: A 716 TYR cc_start: 0.7617 (m-80) cc_final: 0.6703 (m-80) REVERT: A 840 TYR cc_start: 0.7432 (m-10) cc_final: 0.7148 (m-10) REVERT: A 993 TYR cc_start: 0.7125 (m-80) cc_final: 0.3862 (t80) REVERT: A 1349 TYR cc_start: 0.7574 (m-80) cc_final: 0.6870 (m-80) outliers start: 16 outliers final: 10 residues processed: 100 average time/residue: 0.1819 time to fit residues: 28.1168 Evaluate side-chains 100 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain A residue 1140 CYS Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1887 LEU Chi-restraints excluded: chain A residue 1937 MET Chi-restraints excluded: chain A residue 1944 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 72 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 112 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 53 optimal weight: 0.2980 chunk 52 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1524 ASN ** A1666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.216810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.195330 restraints weight = 30205.231| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 1.34 r_work: 0.3937 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3919 r_free = 0.3919 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3919 r_free = 0.3919 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12156 Z= 0.101 Angle : 0.466 10.003 16373 Z= 0.246 Chirality : 0.054 1.700 1708 Planarity : 0.003 0.039 2056 Dihedral : 3.848 56.213 1530 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.93 % Allowed : 8.94 % Favored : 90.13 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.24), residues: 1363 helix: 2.62 (0.18), residues: 816 sheet: 0.16 (2.03), residues: 10 loop : -2.51 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1890 TYR 0.012 0.001 TYR A1305 PHE 0.010 0.001 PHE A 650 TRP 0.017 0.001 TRP A 213 HIS 0.002 0.000 HIS A1666 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (12120) covalent geometry : angle 0.45027 / 0.24 (16291) SS BOND : bond 0.00288 / 0.20 ( 26) SS BOND : angle 1.90216 / 0.89 ( 52) hydrogen bonds : bond 0.03981 / 2.81 ( 625) hydrogen bonds : angle 3.31858 / 2.36 ( 1866) link_BETA1-3 : bond 0.00194 / 0.11 ( 5) link_BETA1-3 : angle 1.04934 / 0.58 ( 15) link_BETA1-4 : bond 0.00377 / 0.20 ( 5) link_BETA1-4 : angle 1.86151 / 0.91 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 36 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue VAL 591 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue ILE 617 is missing expected H atoms. Skipping. Residue ILE 618 is missing expected H atoms. Skipping. Residue ALA 619 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue LEU 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LYS 640 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue ILE 678 is missing expected H atoms. Skipping. Residue LEU 719 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 824 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 828 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue TYR 834 is missing expected H atoms. Skipping. Residue TYR 837 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 839 is missing expected H atoms. Skipping. Residue TYR 840 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue ALA 844 is missing expected H atoms. Skipping. Residue LYS 849 is missing expected H atoms. Skipping. Residue ALA 850 is missing expected H atoms. Skipping. Residue THR 852 is missing expected H atoms. Skipping. Residue THR 887 is missing expected H atoms. Skipping. Residue SER 889 is missing expected H atoms. Skipping. Residue SER 890 is missing expected H atoms. Skipping. Residue TYR 891 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 894 is missing expected H atoms. Skipping. Residue VAL 895 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue TYR 972 is missing expected H atoms. Skipping. Residue SER 977 is missing expected H atoms. Skipping. Residue SER 1092 is missing expected H atoms. Skipping. Residue THR 1180 is missing expected H atoms. Skipping. Residue SER 1183 is missing expected H atoms. Skipping. Residue LYS 1185 is missing expected H atoms. Skipping. Residue LEU 1186 is missing expected H atoms. Skipping. Residue ALA 1189 is missing expected H atoms. Skipping. Residue LYS 1191 is missing expected H atoms. Skipping. Residue SER 1198 is missing expected H atoms. Skipping. Residue THR 1199 is missing expected H atoms. Skipping. Residue SER 1213 is missing expected H atoms. Skipping. Residue ILE 1216 is missing expected H atoms. Skipping. Residue ILE 1225 is missing expected H atoms. Skipping. Residue SER 1286 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Residue MET 1318 is missing expected H atoms. Skipping. Residue SER 1331 is missing expected H atoms. Skipping. Residue TYR 1363 is missing expected H atoms. Skipping. Residue LYS 1422 is missing expected H atoms. Skipping. Residue THR 1425 is missing expected H atoms. Skipping. Residue SER 1427 is missing expected H atoms. Skipping. Residue ILE 1433 is missing expected H atoms. Skipping. Residue LYS 1464 is missing expected H atoms. Skipping. Residue LYS 1626 is missing expected H atoms. Skipping. Residue ILE 1629 is missing expected H atoms. Skipping. Residue THR 1630 is missing expected H atoms. Skipping. Residue LYS 1634 is missing expected H atoms. Skipping. Residue ALA 1657 is missing expected H atoms. Skipping. Residue TYR 1663 is missing expected H atoms. Skipping. Residue LEU 1664 is missing expected H atoms. Skipping. Residue LYS 1711 is missing expected H atoms. Skipping. Residue LYS 1759 is missing expected H atoms. Skipping. Residue ILE 1761 is missing expected H atoms. Skipping. Residue THR 1841 is missing expected H atoms. Skipping. Residue TYR 1862 is missing expected H atoms. Skipping. Residue SER 1911 is missing expected H atoms. Skipping. Residue LYS 1939 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 ASP cc_start: 0.1617 (OUTLIER) cc_final: 0.0391 (t0) REVERT: A 573 GLU cc_start: 0.7801 (tp30) cc_final: 0.7560 (tp30) REVERT: A 716 TYR cc_start: 0.7587 (m-80) cc_final: 0.6680 (m-80) REVERT: A 993 TYR cc_start: 0.7034 (m-80) cc_final: 0.3757 (t80) REVERT: A 1349 TYR cc_start: 0.7541 (m-80) cc_final: 0.6842 (m-80) outliers start: 12 outliers final: 10 residues processed: 92 average time/residue: 0.1939 time to fit residues: 27.1824 Evaluate side-chains 98 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain A residue 1140 CYS Chi-restraints excluded: chain A residue 1524 ASN Chi-restraints excluded: chain A residue 1887 LEU Chi-restraints excluded: chain A residue 1937 MET Chi-restraints excluded: chain A residue 1944 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 68 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.216541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.194339 restraints weight = 30622.796| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 1.35 r_work: 0.3929 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3909 r_free = 0.3909 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3909 r_free = 0.3909 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.142 12156 Z= 0.148 Angle : 0.747 59.200 16373 Z= 0.440 Chirality : 0.054 1.700 1708 Planarity : 0.003 0.038 2056 Dihedral : 3.866 56.270 1530 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.77 % Allowed : 9.18 % Favored : 90.05 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.24), residues: 1363 helix: 2.62 (0.18), residues: 816 sheet: 0.17 (2.02), residues: 10 loop : -2.51 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 132 TYR 0.014 0.001 TYR A1525 PHE 0.011 0.001 PHE A 650 TRP 0.015 0.001 TRP A 213 HIS 0.002 0.000 HIS A1666 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (12120) covalent geometry : angle 0.73892 / 0.44 (16291) SS BOND : bond 0.00280 / 0.19 ( 26) SS BOND : angle 1.80831 / 0.86 ( 52) hydrogen bonds : bond 0.04012 / 2.83 ( 625) hydrogen bonds : angle 3.32445 / 2.37 ( 1866) link_BETA1-3 : bond 0.00225 / 0.13 ( 5) link_BETA1-3 : angle 1.17705 / 0.66 ( 15) link_BETA1-4 : bond 0.00385 / 0.20 ( 5) link_BETA1-4 : angle 1.90186 / 0.93 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2726 Ramachandran restraints generated. 1363 Oldfield, 0 Emsley, 1363 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 36 is missing expected H atoms. Skipping. Residue TYR 44 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue MET 104 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue VAL 114 is missing expected H atoms. Skipping. Residue LYS 120 is missing expected H atoms. Skipping. Residue ILE 161 is missing expected H atoms. Skipping. Residue ALA 162 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue ALA 229 is missing expected H atoms. Skipping. Residue SER 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue THR 347 is missing expected H atoms. Skipping. Residue LYS 374 is missing expected H atoms. Skipping. Residue VAL 591 is missing expected H atoms. Skipping. Residue LEU 612 is missing expected H atoms. Skipping. Residue LEU 613 is missing expected H atoms. Skipping. Residue LYS 614 is missing expected H atoms. Skipping. Residue ILE 617 is missing expected H atoms. Skipping. Residue ILE 618 is missing expected H atoms. Skipping. Residue ALA 619 is missing expected H atoms. Skipping. Residue ALA 620 is missing expected H atoms. Skipping. Residue LYS 625 is missing expected H atoms. Skipping. Residue LEU 627 is missing expected H atoms. Skipping. Residue LYS 628 is missing expected H atoms. Skipping. Residue SER 630 is missing expected H atoms. Skipping. Residue LYS 640 is missing expected H atoms. Skipping. Residue LYS 641 is missing expected H atoms. Skipping. Residue LYS 677 is missing expected H atoms. Skipping. Residue ILE 678 is missing expected H atoms. Skipping. Residue LEU 719 is missing expected H atoms. Skipping. Residue LYS 770 is missing expected H atoms. Skipping. Residue LYS 804 is missing expected H atoms. Skipping. Residue SER 824 is missing expected H atoms. Skipping. Residue SER 825 is missing expected H atoms. Skipping. Residue VAL 827 is missing expected H atoms. Skipping. Residue LYS 828 is missing expected H atoms. Skipping. Residue ILE 833 is missing expected H atoms. Skipping. Residue TYR 834 is missing expected H atoms. Skipping. Residue TYR 837 is missing expected H atoms. Skipping. Residue SER 838 is missing expected H atoms. Skipping. Residue LYS 839 is missing expected H atoms. Skipping. Residue TYR 840 is missing expected H atoms. Skipping. Residue ILE 841 is missing expected H atoms. Skipping. Residue ALA 844 is missing expected H atoms. Skipping. Residue LYS 849 is missing expected H atoms. Skipping. Residue ALA 850 is missing expected H atoms. Skipping. Residue THR 852 is missing expected H atoms. Skipping. Residue THR 887 is missing expected H atoms. Skipping. Residue SER 889 is missing expected H atoms. Skipping. Residue SER 890 is missing expected H atoms. Skipping. Residue TYR 891 is missing expected H atoms. Skipping. Residue LEU 892 is missing expected H atoms. Skipping. Residue SER 893 is missing expected H atoms. Skipping. Residue ILE 894 is missing expected H atoms. Skipping. Residue VAL 895 is missing expected H atoms. Skipping. Residue LEU 896 is missing expected H atoms. Skipping. Residue TYR 972 is missing expected H atoms. Skipping. Residue SER 977 is missing expected H atoms. Skipping. Residue SER 1092 is missing expected H atoms. Skipping. Residue THR 1180 is missing expected H atoms. Skipping. Residue SER 1183 is missing expected H atoms. Skipping. Residue LYS 1185 is missing expected H atoms. Skipping. Residue LEU 1186 is missing expected H atoms. Skipping. Residue ALA 1189 is missing expected H atoms. Skipping. Residue LYS 1191 is missing expected H atoms. Skipping. Residue SER 1198 is missing expected H atoms. Skipping. Residue THR 1199 is missing expected H atoms. Skipping. Residue SER 1213 is missing expected H atoms. Skipping. Residue ILE 1216 is missing expected H atoms. Skipping. Residue ILE 1225 is missing expected H atoms. Skipping. Residue SER 1286 is missing expected H atoms. Skipping. Residue LYS 1308 is missing expected H atoms. Skipping. Residue MET 1318 is missing expected H atoms. Skipping. Residue SER 1331 is missing expected H atoms. Skipping. Residue TYR 1363 is missing expected H atoms. Skipping. Residue LYS 1422 is missing expected H atoms. Skipping. Residue THR 1425 is missing expected H atoms. Skipping. Residue SER 1427 is missing expected H atoms. Skipping. Residue ILE 1433 is missing expected H atoms. Skipping. Residue LYS 1464 is missing expected H atoms. Skipping. Residue LYS 1626 is missing expected H atoms. Skipping. Residue ILE 1629 is missing expected H atoms. Skipping. Residue THR 1630 is missing expected H atoms. Skipping. Residue LYS 1634 is missing expected H atoms. Skipping. Residue ALA 1657 is missing expected H atoms. Skipping. Residue TYR 1663 is missing expected H atoms. Skipping. Residue LEU 1664 is missing expected H atoms. Skipping. Residue LYS 1711 is missing expected H atoms. Skipping. Residue LYS 1759 is missing expected H atoms. Skipping. Residue ILE 1761 is missing expected H atoms. Skipping. Residue THR 1841 is missing expected H atoms. Skipping. Residue TYR 1862 is missing expected H atoms. Skipping. Residue SER 1911 is missing expected H atoms. Skipping. Residue LYS 1939 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 ASP cc_start: 0.1700 (OUTLIER) cc_final: 0.0427 (t0) REVERT: A 716 TYR cc_start: 0.7592 (m-80) cc_final: 0.6682 (m-80) REVERT: A 993 TYR cc_start: 0.7056 (m-80) cc_final: 0.3772 (t80) REVERT: A 1349 TYR cc_start: 0.7564 (m-80) cc_final: 0.6866 (m-80) outliers start: 10 outliers final: 9 residues processed: 93 average time/residue: 0.1961 time to fit residues: 27.5662 Evaluate side-chains 97 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 797 CYS Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1002 ASP Chi-restraints excluded: chain A residue 1140 CYS Chi-restraints excluded: chain A residue 1887 LEU Chi-restraints excluded: chain A residue 1937 MET Chi-restraints excluded: chain A residue 1944 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 74 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 56 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.0050 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.216480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.195874 restraints weight = 30451.607| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 1.37 r_work: 0.3946 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3931 r_free = 0.3931 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3931 r_free = 0.3931 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.142 12156 Z= 0.148 Angle : 0.747 59.200 16373 Z= 0.440 Chirality : 0.054 1.700 1708 Planarity : 0.003 0.038 2056 Dihedral : 3.866 56.270 1530 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.77 % Allowed : 9.10 % Favored : 90.13 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.24), residues: 1363 helix: 2.62 (0.18), residues: 816 sheet: 0.17 (2.02), residues: 10 loop : -2.51 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 132 TYR 0.014 0.001 TYR A1525 PHE 0.011 0.001 PHE A 650 TRP 0.015 0.001 TRP A 213 HIS 0.002 0.000 HIS A1666 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (12120) covalent geometry : angle 0.73892 / 0.44 (16291) SS BOND : bond 0.00280 / 0.19 ( 26) SS BOND : angle 1.80831 / 0.86 ( 52) hydrogen bonds : bond 0.04012 / 2.83 ( 625) hydrogen bonds : angle 3.32445 / 2.37 ( 1866) link_BETA1-3 : bond 0.00225 / 0.13 ( 5) link_BETA1-3 : angle 1.17705 / 0.66 ( 15) link_BETA1-4 : bond 0.00385 / 0.20 ( 5) link_BETA1-4 : angle 1.90186 / 0.93 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4146.82 seconds wall clock time: 71 minutes 28.99 seconds (4288.99 seconds total)