Starting phenix.real_space_refine on Mon Apr 6 15:05:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jgh_22327/04_2026/7jgh_22327.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jgh_22327/04_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 { model { file = "/net/cci-nas-00/data/ceres_data/7jgh_22327/04_2026/7jgh_22327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jgh_22327/04_2026/7jgh_22327.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jgh_22327/04_2026/7jgh_22327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jgh_22327/04_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/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 dihedrals: 34 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 dihedrals: 4 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: 3.27, per 1000 atoms: 0.17 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: 1.80 Conformation dependent library (CDL) restraints added in 598.7 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: 3.49 Time building geometry restraints manager: 2.44 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: 9354 17.92 - 35.83: 581 35.83 - 53.75: 154 53.75 - 71.66: 45 71.66 - 89.58: 8 Dihedral angle restraints: 10142 sinusoidal: 5380 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 10139 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.230 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5985 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 : 12.270 89.581 4798 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 covalent geometry : bond 0.00667 (12120) covalent geometry : angle 0.82779 (16291) SS BOND : bond 0.00269 ( 26) SS BOND : angle 1.31100 ( 52) hydrogen bonds : bond 0.15338 ( 625) hydrogen bonds : angle 5.10444 ( 1866) link_BETA1-3 : bond 0.07874 ( 5) link_BETA1-3 : angle 3.05900 ( 15) link_BETA1-4 : bond 0.08191 ( 5) link_BETA1-4 : angle 21.70953 ( 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 : 0.515 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: 0.1695 time to fit residues: 27.1356 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 : 0.481 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4481 r_free = 0.4481 target = 0.234780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.220119 restraints weight = 30362.287| |-----------------------------------------------------------------------------| r_work (start): 0.4367 rms_B_bonded: 1.02 r_work: 0.4234 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.4135 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4201 r_free = 0.4201 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4198 r_free = 0.4198 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12156 Z= 0.133 Angle : 0.531 9.890 16373 Z= 0.269 Chirality : 0.055 1.690 1708 Planarity : 0.003 0.034 2056 Dihedral : 8.076 78.977 1792 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.69 % Allowed : 5.24 % Favored : 94.06 % 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: 0.81 (0.24), residues: 1363 helix: 2.42 (0.18), residues: 813 sheet: -0.64 (1.81), residues: 10 loop : -2.63 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1792 TYR 0.016 0.001 TYR A1649 PHE 0.012 0.001 PHE A1138 TRP 0.009 0.001 TRP A 718 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00285 (12120) covalent geometry : angle 0.50462 (16291) SS BOND : bond 0.00397 ( 26) SS BOND : angle 1.83867 ( 52) hydrogen bonds : bond 0.04091 ( 625) hydrogen bonds : angle 3.58515 ( 1866) link_BETA1-3 : bond 0.00567 ( 5) link_BETA1-3 : angle 1.44843 ( 15) link_BETA1-4 : bond 0.00865 ( 5) link_BETA1-4 : angle 4.18008 ( 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 103 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.7921 (m-80) cc_final: 0.7392 (m-80) REVERT: A 64 ASP cc_start: 0.4757 (m-30) cc_final: 0.4448 (m-30) REVERT: A 716 TYR cc_start: 0.6811 (m-80) cc_final: 0.6293 (m-80) REVERT: A 721 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.6322 (mtm) REVERT: A 993 TYR cc_start: 0.4719 (m-10) cc_final: 0.3242 (p90) REVERT: A 1578 CYS cc_start: 0.4505 (m) cc_final: 0.4187 (m) outliers start: 9 outliers final: 7 residues processed: 97 average time/residue: 0.1566 time to fit residues: 23.7134 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 : 0.491 ------------------------------------------------------------------------------- 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 1041 MET Chi-restraints excluded: chain A residue 1140 CYS 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: 1.9990 chunk 53 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 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: 0.0770 chunk 26 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 571 GLN ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1538 ASN A1641 GLN A1942 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.220245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.212017 restraints weight = 30313.394| |-----------------------------------------------------------------------------| r_work (start): 0.4438 rms_B_bonded: 0.51 r_work: 0.4346 rms_B_bonded: 0.83 restraints_weight: 0.5000 r_work: 0.4223 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4034 r_free = 0.4034 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4034 r_free = 0.4034 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12156 Z= 0.151 Angle : 0.533 9.998 16373 Z= 0.280 Chirality : 0.056 1.696 1708 Planarity : 0.003 0.039 2056 Dihedral : 6.677 66.132 1792 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 1.46 % Allowed : 5.63 % Favored : 92.91 % 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: 0.87 (0.24), residues: 1363 helix: 2.47 (0.18), residues: 814 sheet: -0.25 (1.91), residues: 10 loop : -2.64 (0.24), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 230 TYR 0.018 0.001 TYR A1305 PHE 0.014 0.001 PHE A 650 TRP 0.013 0.001 TRP A 213 HIS 0.004 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00326 (12120) covalent geometry : angle 0.51358 (16291) SS BOND : bond 0.00311 ( 26) SS BOND : angle 1.55396 ( 52) hydrogen bonds : bond 0.04474 ( 625) hydrogen bonds : angle 3.47040 ( 1866) link_BETA1-3 : bond 0.00278 ( 5) link_BETA1-3 : angle 1.55434 ( 15) link_BETA1-4 : bond 0.00546 ( 5) link_BETA1-4 : angle 3.59908 ( 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 117 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 716 TYR cc_start: 0.7009 (m-80) cc_final: 0.6151 (m-80) REVERT: A 939 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8606 (p0) REVERT: A 993 TYR cc_start: 0.5867 (m-10) cc_final: 0.2272 (p90) REVERT: A 1551 ASP cc_start: 0.6331 (t0) cc_final: 0.6075 (t0) REVERT: A 1578 CYS cc_start: 0.4999 (m) cc_final: 0.4712 (m) REVERT: A 1887 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7738 (mm) outliers start: 19 outliers final: 10 residues processed: 107 average time/residue: 0.1580 time to fit residues: 25.6507 Evaluate side-chains 101 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 763 GLU Chi-restraints excluded: chain A residue 873 ILE Chi-restraints excluded: chain A residue 900 ILE 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 126 optimal weight: 0.0570 chunk 81 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 125 optimal weight: 0.0060 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 ASN A1150 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.238709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.222197 restraints weight = 29472.031| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 1.02 r_work: 0.4243 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.4155 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3993 r_free = 0.3993 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3993 r_free = 0.3993 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12156 Z= 0.090 Angle : 0.452 10.075 16373 Z= 0.232 Chirality : 0.053 1.696 1708 Planarity : 0.003 0.032 2056 Dihedral : 5.928 54.410 1792 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.08 % Allowed : 7.02 % Favored : 91.90 % 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: 1.13 (0.24), residues: 1363 helix: 2.68 (0.18), residues: 816 sheet: 0.34 (2.03), residues: 10 loop : -2.56 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 132 TYR 0.015 0.001 TYR A1305 PHE 0.010 0.001 PHE A 650 TRP 0.010 0.001 TRP A 213 HIS 0.002 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00190 (12120) covalent geometry : angle 0.43416 (16291) SS BOND : bond 0.00208 ( 26) SS BOND : angle 1.45961 ( 52) hydrogen bonds : bond 0.03819 ( 625) hydrogen bonds : angle 3.28181 ( 1866) link_BETA1-3 : bond 0.00310 ( 5) link_BETA1-3 : angle 1.24378 ( 15) link_BETA1-4 : bond 0.00477 ( 5) link_BETA1-4 : angle 2.99884 ( 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 102 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 GLU cc_start: 0.7576 (tp30) cc_final: 0.7341 (tp30) REVERT: A 716 TYR cc_start: 0.7204 (m-80) cc_final: 0.6340 (m-80) REVERT: A 721 MET cc_start: 0.6915 (OUTLIER) cc_final: 0.6559 (mtm) REVERT: A 993 TYR cc_start: 0.6086 (OUTLIER) cc_final: 0.2065 (p90) outliers start: 14 outliers final: 9 residues processed: 93 average time/residue: 0.1598 time to fit residues: 23.1670 Evaluate side-chains 97 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 763 GLU 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 993 TYR Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1088 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 117 optimal weight: 1.9990 chunk 41 optimal weight: 0.0020 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 125 optimal weight: 0.0980 chunk 47 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 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 = 0.4359 r_free = 0.4359 target = 0.221617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.204903 restraints weight = 29882.711| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 1.31 r_work: 0.4110 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.4019 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3994 r_free = 0.3994 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3994 r_free = 0.3994 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.2365 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= 0.083 Angle : 0.427 10.129 16373 Z= 0.218 Chirality : 0.053 1.699 1708 Planarity : 0.002 0.032 2056 Dihedral : 4.862 53.094 1792 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.08 % Allowed : 7.02 % Favored : 91.90 % 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: 1.35 (0.24), residues: 1363 helix: 2.88 (0.18), residues: 816 sheet: 0.02 (1.93), residues: 10 loop : -2.51 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1758 TYR 0.013 0.001 TYR A1305 PHE 0.007 0.001 PHE A1774 TRP 0.010 0.001 TRP A 213 HIS 0.002 0.000 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00177 (12120) covalent geometry : angle 0.41298 (16291) SS BOND : bond 0.00212 ( 26) SS BOND : angle 1.22201 ( 52) hydrogen bonds : bond 0.03505 ( 625) hydrogen bonds : angle 3.11709 ( 1866) link_BETA1-3 : bond 0.00252 ( 5) link_BETA1-3 : angle 1.31394 ( 15) link_BETA1-4 : bond 0.00498 ( 5) link_BETA1-4 : angle 2.59901 ( 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: 14 poor density : 94 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7584 (tpt170) cc_final: 0.7133 (tpt170) REVERT: A 716 TYR cc_start: 0.7212 (m-80) cc_final: 0.6318 (m-80) REVERT: A 721 MET cc_start: 0.6842 (OUTLIER) cc_final: 0.6498 (mtm) outliers start: 14 outliers final: 11 residues processed: 100 average time/residue: 0.1734 time to fit residues: 25.8425 Evaluate side-chains 100 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 TYR 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 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: 0.9990 chunk 38 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 118 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1443 GLN A1504 GLN A1666 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.212269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.198053 restraints weight = 30447.928| |-----------------------------------------------------------------------------| r_work (start): 0.4157 rms_B_bonded: 0.91 r_work: 0.4017 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3883 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3825 r_free = 0.3825 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3825 r_free = 0.3825 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12156 Z= 0.137 Angle : 0.501 9.954 16373 Z= 0.264 Chirality : 0.055 1.697 1708 Planarity : 0.003 0.037 2056 Dihedral : 4.755 56.682 1792 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.16 % Allowed : 7.40 % Favored : 91.44 % 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: 1.14 (0.24), residues: 1363 helix: 2.69 (0.18), residues: 816 sheet: 0.63 (2.09), residues: 10 loop : -2.56 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 230 TYR 0.022 0.002 TYR A 574 PHE 0.014 0.001 PHE A 650 TRP 0.015 0.001 TRP A 213 HIS 0.004 0.001 HIS A1666 Details of bonding type rmsd covalent geometry : bond 0.00303 (12120) covalent geometry : angle 0.48796 (16291) SS BOND : bond 0.00284 ( 26) SS BOND : angle 1.39629 ( 52) hydrogen bonds : bond 0.04137 ( 625) hydrogen bonds : angle 3.33444 ( 1866) link_BETA1-3 : bond 0.00183 ( 5) link_BETA1-3 : angle 1.33270 ( 15) link_BETA1-4 : bond 0.00400 ( 5) link_BETA1-4 : angle 2.63235 ( 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 105 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7874 (tpt170) cc_final: 0.7370 (tpt170) REVERT: A 573 GLU cc_start: 0.7736 (tp30) cc_final: 0.7487 (tp30) REVERT: A 716 TYR cc_start: 0.7437 (m-80) cc_final: 0.6585 (m-80) outliers start: 15 outliers final: 11 residues processed: 97 average time/residue: 0.1631 time to fit residues: 24.2252 Evaluate side-chains 93 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1140 CYS Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1168 ILE 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: 0.9990 chunk 139 optimal weight: 0.9990 chunk 110 optimal weight: 0.0970 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.220494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.197467 restraints weight = 30501.586| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 1.56 r_work: 0.4017 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3900 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3889 r_free = 0.3889 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3889 r_free = 0.3889 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.3086 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= 0.114 Angle : 0.468 10.000 16373 Z= 0.246 Chirality : 0.054 1.698 1708 Planarity : 0.003 0.037 2056 Dihedral : 4.615 56.064 1792 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.31 % Allowed : 7.48 % 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: 1.16 (0.24), residues: 1363 helix: 2.71 (0.18), residues: 816 sheet: 0.34 (2.03), residues: 10 loop : -2.57 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 132 TYR 0.015 0.001 TYR A1305 PHE 0.011 0.001 PHE A 650 TRP 0.015 0.001 TRP A 213 HIS 0.002 0.001 HIS A 142 Details of bonding type rmsd covalent geometry : bond 0.00249 (12120) covalent geometry : angle 0.45386 (16291) SS BOND : bond 0.00248 ( 26) SS BOND : angle 1.46320 ( 52) hydrogen bonds : bond 0.03996 ( 625) hydrogen bonds : angle 3.29306 ( 1866) link_BETA1-3 : bond 0.00245 ( 5) link_BETA1-3 : angle 1.29479 ( 15) link_BETA1-4 : bond 0.00436 ( 5) link_BETA1-4 : angle 2.53762 ( 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: 17 poor density : 87 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 716 TYR cc_start: 0.7628 (m-80) cc_final: 0.6703 (m-80) REVERT: A 721 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6918 (mtm) REVERT: A 993 TYR cc_start: 0.7242 (m-80) cc_final: 0.3387 (t80) REVERT: A 1349 TYR cc_start: 0.7629 (m-80) cc_final: 0.7026 (m-80) outliers start: 17 outliers final: 12 residues processed: 95 average time/residue: 0.1555 time to fit residues: 22.7343 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 : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 567 GLU Chi-restraints excluded: chain A residue 721 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 61 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 0.0980 chunk 45 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1524 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.220107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.196749 restraints weight = 30544.133| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 1.62 r_work: 0.4009 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3892 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3885 r_free = 0.3885 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3885 r_free = 0.3885 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.3252 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= 0.107 Angle : 0.455 9.996 16373 Z= 0.238 Chirality : 0.054 1.699 1708 Planarity : 0.003 0.037 2056 Dihedral : 4.470 56.011 1792 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.08 % Allowed : 8.02 % Favored : 90.90 % 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: 1.20 (0.24), residues: 1363 helix: 2.71 (0.18), residues: 819 sheet: 0.26 (2.00), residues: 10 loop : -2.51 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 132 TYR 0.013 0.001 TYR A1305 PHE 0.010 0.001 PHE A 650 TRP 0.016 0.001 TRP A 213 HIS 0.002 0.000 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00235 (12120) covalent geometry : angle 0.44147 (16291) SS BOND : bond 0.00312 ( 26) SS BOND : angle 1.37352 ( 52) hydrogen bonds : bond 0.03864 ( 625) hydrogen bonds : angle 3.24313 ( 1866) link_BETA1-3 : bond 0.00266 ( 5) link_BETA1-3 : angle 1.25513 ( 15) link_BETA1-4 : bond 0.00455 ( 5) link_BETA1-4 : angle 2.43802 ( 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 104 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7553 (tpt170) cc_final: 0.7119 (tpt170) REVERT: A 716 TYR cc_start: 0.7689 (m-80) cc_final: 0.6754 (m-80) REVERT: A 993 TYR cc_start: 0.7235 (m-80) cc_final: 0.3463 (t80) REVERT: A 1349 TYR cc_start: 0.7638 (m-80) cc_final: 0.7109 (m-80) REVERT: A 1563 TYR cc_start: 0.8355 (t80) cc_final: 0.8072 (t80) outliers start: 14 outliers final: 11 residues processed: 96 average time/residue: 0.1633 time to fit residues: 23.7649 Evaluate side-chains 99 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 63 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1524 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.216469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.194073 restraints weight = 30274.580| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 1.38 r_work: 0.3923 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3901 r_free = 0.3901 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3901 r_free = 0.3901 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.3447 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= 0.121 Angle : 0.486 11.915 16373 Z= 0.256 Chirality : 0.054 1.698 1708 Planarity : 0.003 0.038 2056 Dihedral : 4.497 56.646 1792 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.08 % Allowed : 8.17 % Favored : 90.75 % 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: 1.16 (0.24), residues: 1363 helix: 2.65 (0.18), residues: 820 sheet: 0.43 (2.05), residues: 10 loop : -2.50 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 132 TYR 0.012 0.001 TYR A1305 PHE 0.011 0.001 PHE A 650 TRP 0.017 0.001 TRP A 213 HIS 0.002 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00268 (12120) covalent geometry : angle 0.46272 (16291) SS BOND : bond 0.00519 ( 26) SS BOND : angle 2.27962 ( 52) hydrogen bonds : bond 0.04024 ( 625) hydrogen bonds : angle 3.32241 ( 1866) link_BETA1-3 : bond 0.00228 ( 5) link_BETA1-3 : angle 1.25896 ( 15) link_BETA1-4 : bond 0.00404 ( 5) link_BETA1-4 : angle 2.41050 ( 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 103 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7670 (tpt170) cc_final: 0.7240 (tpt170) REVERT: A 716 TYR cc_start: 0.7613 (m-80) cc_final: 0.6710 (m-80) REVERT: A 993 TYR cc_start: 0.7148 (m-80) cc_final: 0.2079 (p90) REVERT: A 1349 TYR cc_start: 0.7576 (m-80) cc_final: 0.6816 (m-80) REVERT: A 1785 ILE cc_start: 0.9067 (pt) cc_final: 0.8661 (mt) outliers start: 14 outliers final: 12 residues processed: 96 average time/residue: 0.1626 time to fit residues: 23.7050 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 : 0.536 ------------------------------------------------------------------------------- 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 1140 CYS Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1524 ASN Chi-restraints excluded: chain A residue 1887 LEU 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: 0.1980 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** 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 = 0.4350 r_free = 0.4350 target = 0.218291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.197367 restraints weight = 30448.954| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 1.32 r_work: 0.3930 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3894 r_free = 0.3894 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3894 r_free = 0.3894 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 12156 Z= 0.155 Angle : 0.757 59.200 16373 Z= 0.446 Chirality : 0.054 1.699 1708 Planarity : 0.003 0.038 2056 Dihedral : 4.502 56.639 1792 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.85 % Allowed : 8.56 % Favored : 90.59 % 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: 1.16 (0.24), residues: 1363 helix: 2.65 (0.18), residues: 820 sheet: 0.42 (2.05), residues: 10 loop : -2.51 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 583 TYR 0.015 0.001 TYR A1525 PHE 0.011 0.001 PHE A 650 TRP 0.016 0.001 TRP A 213 HIS 0.001 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00317 (12120) covalent geometry : angle 0.74506 (16291) SS BOND : bond 0.00340 ( 26) SS BOND : angle 2.10255 ( 52) hydrogen bonds : bond 0.04021 ( 625) hydrogen bonds : angle 3.32281 ( 1866) link_BETA1-3 : bond 0.00202 ( 5) link_BETA1-3 : angle 1.25614 ( 15) link_BETA1-4 : bond 0.00365 ( 5) link_BETA1-4 : angle 2.47850 ( 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 97 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7658 (tpt170) cc_final: 0.7230 (tpt170) REVERT: A 716 TYR cc_start: 0.7605 (m-80) cc_final: 0.6700 (m-80) REVERT: A 993 TYR cc_start: 0.7125 (m-80) cc_final: 0.2076 (p90) REVERT: A 1349 TYR cc_start: 0.7575 (m-80) cc_final: 0.6814 (m-80) REVERT: A 1785 ILE cc_start: 0.9067 (pt) cc_final: 0.8656 (mt) outliers start: 11 outliers final: 11 residues processed: 91 average time/residue: 0.1696 time to fit residues: 23.1059 Evaluate side-chains 97 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 74 optimal weight: 0.0770 chunk 1 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 631 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 782 ASN ** 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 = 0.4333 r_free = 0.4333 target = 0.216582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.195151 restraints weight = 30458.070| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 1.40 r_work: 0.3927 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3927 ------------------------------------------------------------------------------- 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 = 0.26 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 | |-----------------------------------------------------------------------------| r_final: 0.3909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 12156 Z= 0.155 Angle : 0.757 59.200 16373 Z= 0.446 Chirality : 0.054 1.699 1708 Planarity : 0.003 0.038 2056 Dihedral : 4.502 56.639 1792 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.85 % Allowed : 8.56 % Favored : 90.59 % 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: 1.16 (0.24), residues: 1363 helix: 2.65 (0.18), residues: 820 sheet: 0.42 (2.05), residues: 10 loop : -2.51 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 583 TYR 0.015 0.001 TYR A1525 PHE 0.011 0.001 PHE A 650 TRP 0.016 0.001 TRP A 213 HIS 0.001 0.001 HIS A 631 Details of bonding type rmsd covalent geometry : bond 0.00317 (12120) covalent geometry : angle 0.74506 (16291) SS BOND : bond 0.00340 ( 26) SS BOND : angle 2.10255 ( 52) hydrogen bonds : bond 0.04021 ( 625) hydrogen bonds : angle 3.32281 ( 1866) link_BETA1-3 : bond 0.00202 ( 5) link_BETA1-3 : angle 1.25614 ( 15) link_BETA1-4 : bond 0.00365 ( 5) link_BETA1-4 : angle 2.47849 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3995.99 seconds wall clock time: 68 minutes 58.77 seconds (4138.77 seconds total)