Starting phenix.real_space_refine on Fri Jul 3 14:33:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xvf_33485/07_2026/7xvf_33485.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xvf_33485/07_2026/7xvf_33485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xvf_33485/07_2026/7xvf_33485.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xvf_33485/07_2026/7xvf_33485.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xvf_33485/07_2026/7xvf_33485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xvf_33485/07_2026/7xvf_33485.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xvf_33485/07_2026/7xvf_33485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xvf_33485/07_2026/7xvf_33485.map" } resolution = 2.8 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= 0.007 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 26 5.49 5 S 100 5.16 5 C 9037 2.51 5 N 2028 2.21 5 O 2434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13625 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1261, 10100 Classifications: {'peptide': 1261} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 1219} Chain breaks: 6 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASN:plan1': 3, 'GLN:plan1': 2, 'ARG:plan': 2, 'TYR:plan': 1, 'GLU:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 980 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 986 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 32, 942 Unusual residues: {'1PW': 1, 'CLR': 1, 'LPE': 16, 'NAG': 2, 'PCW': 6, 'Y01': 5} Classifications: {'peptide': 1, 'undetermined': 31} Link IDs: {None: 31} Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'1PW:plan-1': 1, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 32, 942 Unusual residues: {'1PW': 1, 'CLR': 1, 'LPE': 16, 'NAG': 2, 'PCW': 6, 'Y01': 5} Classifications: {'peptide': 1, 'undetermined': 31} Link IDs: {None: 31} Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'1PW:plan-1': 1, 'PCW:plan-4': 4} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 893 Chain: "B" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 73 Unusual residues: {'LPE': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APCW A2014 " occ=0.50 ... (86 atoms not shown) pdb=" P BPCW A2014 " occ=0.50 Time building chain proxies: 2.98, per 1000 atoms: 0.22 Number of scatterers: 13625 At special positions: 0 Unit cell: (136.395, 145.055, 126.652, 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 100 16.00 P 26 15.00 O 2434 8.00 N 2028 7.00 C 9037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=2.02 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.15 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS C 55 " distance=2.05 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.03 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.04 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=1.98 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.18 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.02 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.04 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2001 " - " ASN A1375 " " NAG A2002 " - " ASN A 283 " " NAG B 301 " - " ASN B 93 " " NAG B 302 " - " ASN B 110 " " NAG B 303 " - " ASN B 114 " " NAG B 304 " - " ASN B 135 " " NAG C 301 " - " ASN C 66 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 572.5 milliseconds 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2950 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 10 sheets defined 67.8% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 16 through 34 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 79 through 85 removed outlier: 3.985A pdb=" N ASP A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.604A pdb=" N ARG A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 144 removed outlier: 4.014A pdb=" N SER A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 175 removed outlier: 4.208A pdb=" N ASN A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 185 Processing helix chain 'A' and resid 186 through 205 Processing helix chain 'A' and resid 210 through 219 removed outlier: 3.578A pdb=" N LEU A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 226 removed outlier: 3.903A pdb=" N LYS A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 245 removed outlier: 3.760A pdb=" N ILE A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 268 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 285 through 293 Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 362 through 375 Processing helix chain 'A' and resid 378 through 389 Processing helix chain 'A' and resid 389 through 417 Processing helix chain 'A' and resid 727 through 741 Processing helix chain 'A' and resid 742 through 762 removed outlier: 3.511A pdb=" N ASP A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LEU A 748 " --> pdb=" O PRO A 744 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 751 " --> pdb=" O ASP A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 798 Processing helix chain 'A' and resid 799 through 806 Processing helix chain 'A' and resid 808 through 824 Processing helix chain 'A' and resid 831 through 835 Processing helix chain 'A' and resid 837 through 848 removed outlier: 3.610A pdb=" N SER A 848 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 895 removed outlier: 4.677A pdb=" N GLY A 864 " --> pdb=" O GLY A 860 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ALA A 865 " --> pdb=" O ASN A 861 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 900 removed outlier: 3.875A pdb=" N ILE A 899 " --> pdb=" O CYS A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 926 Processing helix chain 'A' and resid 928 through 940 Processing helix chain 'A' and resid 940 through 956 removed outlier: 3.775A pdb=" N CYS A 944 " --> pdb=" O GLY A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 972 removed outlier: 3.895A pdb=" N LEU A 964 " --> pdb=" O LEU A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1014 removed outlier: 3.830A pdb=" N ILE A 990 " --> pdb=" O ASN A 986 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A1000 " --> pdb=" O LYS A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1191 Processing helix chain 'A' and resid 1191 through 1212 removed outlier: 3.858A pdb=" N GLU A1212 " --> pdb=" O ALA A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1248 removed outlier: 3.583A pdb=" N LYS A1223 " --> pdb=" O LYS A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1254 Processing helix chain 'A' and resid 1256 through 1279 Processing helix chain 'A' and resid 1283 through 1292 Processing helix chain 'A' and resid 1293 through 1296 Processing helix chain 'A' and resid 1297 through 1304 removed outlier: 4.154A pdb=" N LEU A1301 " --> pdb=" O PRO A1297 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER A1302 " --> pdb=" O LEU A1298 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A1303 " --> pdb=" O ARG A1299 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A1304 " --> pdb=" O ALA A1300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1297 through 1304' Processing helix chain 'A' and resid 1304 through 1316 Processing helix chain 'A' and resid 1317 through 1344 removed outlier: 4.258A pdb=" N ASN A1323 " --> pdb=" O PRO A1319 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL A1324 " --> pdb=" O SER A1320 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1377 removed outlier: 3.743A pdb=" N CYS A1370 " --> pdb=" O ASN A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1404 removed outlier: 3.743A pdb=" N TYR A1396 " --> pdb=" O VAL A1392 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A1397 " --> pdb=" O GLY A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1416 removed outlier: 3.872A pdb=" N ILE A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1432 No H-bonds generated for 'chain 'A' and resid 1430 through 1432' Processing helix chain 'A' and resid 1433 through 1447 removed outlier: 3.733A pdb=" N PHE A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1468 Processing helix chain 'A' and resid 1475 through 1490 removed outlier: 3.563A pdb=" N LYS A1480 " --> pdb=" O GLU A1476 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A1489 " --> pdb=" O MET A1485 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A1490 " --> pdb=" O LYS A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1514 Processing helix chain 'A' and resid 1514 through 1534 removed outlier: 3.858A pdb=" N ASP A1518 " --> pdb=" O ASN A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1570 removed outlier: 3.501A pdb=" N SER A1568 " --> pdb=" O LEU A1564 " (cutoff:3.500A) Processing helix chain 'A' and resid 1571 through 1575 Processing helix chain 'A' and resid 1576 through 1602 Processing helix chain 'A' and resid 1605 through 1613 Processing helix chain 'A' and resid 1616 through 1622 removed outlier: 3.999A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A1622 " --> pdb=" O GLY A1618 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1627 removed outlier: 4.391A pdb=" N GLY A1626 " --> pdb=" O ARG A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1667 removed outlier: 3.635A pdb=" N LEU A1633 " --> pdb=" O GLY A1629 " (cutoff:3.500A) Proline residue: A1642 - end of helix removed outlier: 3.914A pdb=" N ALA A1667 " --> pdb=" O MET A1663 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 3.847A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1709 Proline residue: A1706 - end of helix removed outlier: 3.762A pdb=" N ASN A1709 " --> pdb=" O ALA A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1732 through 1750 removed outlier: 3.621A pdb=" N TYR A1743 " --> pdb=" O TYR A1739 " (cutoff:3.500A) Processing helix chain 'A' and resid 1750 through 1768 Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 153 through 192 removed outlier: 3.677A pdb=" N LYS B 184 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 118 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 91 Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 277 Processing sheet with id=AA3, first strand: chain 'A' and resid 1348 through 1352 Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.303A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N THR B 53 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLU B 74 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA6, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AA7, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.050A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER C 64 " --> pdb=" O MET C 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.050A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE C 129 " --> pdb=" O HIS C 136 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N HIS C 136 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN C 131 " --> pdb=" O ASP C 134 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 46 through 48 Processing sheet with id=AB1, first strand: chain 'C' and resid 81 through 83 814 hydrogen bonds defined for protein. 2328 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1987 1.28 - 1.41: 3425 1.41 - 1.55: 8199 1.55 - 1.68: 141 1.68 - 1.81: 163 Bond restraints: 13915 Sorted by residual: bond pdb=" CBE Y01 A2003 " pdb=" CBI Y01 A2003 " ideal model delta sigma weight residual 1.550 1.337 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" CAQ Y01 A2003 " pdb=" CBG Y01 A2003 " ideal model delta sigma weight residual 1.523 1.334 0.189 2.00e-02 2.50e+03 8.95e+01 bond pdb=" CAI Y01 A2003 " pdb=" CAZ Y01 A2003 " ideal model delta sigma weight residual 1.332 1.512 -0.180 2.00e-02 2.50e+03 8.14e+01 bond pdb=" CBG Y01 A2003 " pdb=" CBI Y01 A2003 " ideal model delta sigma weight residual 1.537 1.712 -0.175 2.00e-02 2.50e+03 7.67e+01 bond pdb=" CAS Y01 A2003 " pdb=" CBF Y01 A2003 " ideal model delta sigma weight residual 1.533 1.688 -0.155 2.00e-02 2.50e+03 6.04e+01 ... (remaining 13910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 17456 2.77 - 5.54: 1037 5.54 - 8.31: 236 8.31 - 11.07: 37 11.07 - 13.84: 11 Bond angle restraints: 18777 Sorted by residual: angle pdb=" N SER A1362 " pdb=" CA SER A1362 " pdb=" C SER A1362 " ideal model delta sigma weight residual 113.97 100.13 13.84 1.28e+00 6.10e-01 1.17e+02 angle pdb=" N GLN A 941 " pdb=" CA GLN A 941 " pdb=" C GLN A 941 " ideal model delta sigma weight residual 111.28 121.78 -10.50 1.09e+00 8.42e-01 9.28e+01 angle pdb=" N SER A 51 " pdb=" CA SER A 51 " pdb=" C SER A 51 " ideal model delta sigma weight residual 112.38 103.42 8.96 1.22e+00 6.72e-01 5.40e+01 angle pdb=" C ASN A 336 " pdb=" N PRO A 337 " pdb=" CA PRO A 337 " ideal model delta sigma weight residual 120.52 113.48 7.04 9.90e-01 1.02e+00 5.05e+01 angle pdb=" N VAL A1720 " pdb=" CA VAL A1720 " pdb=" C VAL A1720 " ideal model delta sigma weight residual 110.62 117.55 -6.93 1.02e+00 9.61e-01 4.61e+01 ... (remaining 18772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.99: 7654 31.99 - 63.99: 559 63.99 - 95.98: 38 95.98 - 127.98: 12 127.98 - 159.97: 6 Dihedral angle restraints: 8269 sinusoidal: 3709 harmonic: 4560 Sorted by residual: dihedral pdb=" CB CYS A 275 " pdb=" SG CYS A 275 " pdb=" SG CYS A 324 " pdb=" CB CYS A 324 " ideal model delta sinusoidal sigma weight residual 93.00 -178.41 -88.59 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CB CYS A 315 " pdb=" SG CYS A 315 " pdb=" SG CYS A 330 " pdb=" CB CYS A 330 " ideal model delta sinusoidal sigma weight residual -86.00 -148.32 62.32 1 1.00e+01 1.00e-02 5.14e+01 dihedral pdb=" CA ASP B 100 " pdb=" C ASP B 100 " pdb=" N LEU B 101 " pdb=" CA LEU B 101 " ideal model delta harmonic sigma weight residual 180.00 -153.91 -26.09 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 8266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 2005 0.151 - 0.302: 92 0.302 - 0.452: 7 0.452 - 0.603: 0 0.603 - 0.754: 1 Chirality restraints: 2105 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.60e+01 chirality pdb=" C1 NAG B 304 " pdb=" ND2 ASN B 135 " pdb=" C2 NAG B 304 " pdb=" O5 NAG B 304 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CBB Y01 A2003 " pdb=" CAC Y01 A2003 " pdb=" CAO Y01 A2003 " pdb=" CBE Y01 A2003 " both_signs ideal model delta sigma weight residual False 2.58 2.96 -0.39 2.00e-01 2.50e+01 3.72e+00 ... (remaining 2102 not shown) Planarity restraints: 2195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.319 2.00e-02 2.50e+03 2.79e-01 9.76e+02 pdb=" C7 NAG E 1 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.094 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.500 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " -0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAH 1PW A2007 " 0.140 2.00e-02 2.50e+03 1.40e-01 1.95e+02 pdb=" CAI 1PW A2007 " 0.140 2.00e-02 2.50e+03 pdb=" CAK 1PW A2007 " -0.140 2.00e-02 2.50e+03 pdb=" CAZ 1PW A2007 " -0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.083 2.00e-02 2.50e+03 6.89e-02 5.93e+01 pdb=" C7 NAG E 2 " 0.022 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.063 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.110 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.014 2.00e-02 2.50e+03 ... (remaining 2192 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1291 2.73 - 3.27: 14117 3.27 - 3.81: 21794 3.81 - 4.36: 27866 4.36 - 4.90: 45515 Nonbonded interactions: 110583 Sorted by model distance: nonbonded pdb=" O3 NAG B 304 " pdb=" O7 NAG B 304 " model vdw 2.186 3.040 nonbonded pdb=" N GLY A1685 " pdb=" O2H LPE A2018 " model vdw 2.234 3.120 nonbonded pdb=" O ILE A 132 " pdb=" OG1 THR A 135 " model vdw 2.242 3.040 nonbonded pdb=" NH2 ARG C 47 " pdb=" O SER C 102 " model vdw 2.281 3.120 nonbonded pdb=" NH2 ARG A 30 " pdb=" OD2 ASP A 84 " model vdw 2.293 3.120 ... (remaining 110578 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 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' } 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=0.41 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: 2.950 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.720 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 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 : 0.015 0.213 13937 Z= 0.973 Angle : 1.631 49.792 18832 Z= 0.961 Chirality : 0.073 0.754 2105 Planarity : 0.010 0.279 2186 Dihedral : 20.178 159.973 5286 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.46 % Allowed : 5.47 % Favored : 94.08 % Rotamer: Outliers : 1.31 % Allowed : 12.55 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.61 (0.20), residues: 1536 helix: -0.58 (0.16), residues: 908 sheet: -0.80 (0.41), residues: 143 loop : -1.86 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 907 TYR 0.029 0.002 TYR A 305 PHE 0.052 0.002 PHE A 15 TRP 0.018 0.002 TRP B 57 HIS 0.012 0.002 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.01492 / 0.97 (13915) covalent geometry : angle 1.57223 / 0.94 (18777) SS BOND : bond 0.05975 / 3.98 ( 11) SS BOND : angle 11.73654 / 4.32 ( 22) hydrogen bonds : bond 0.19157 / 12.46 ( 808) hydrogen bonds : angle 7.54686 / 5.17 ( 2328) link_BETA1-4 : bond 0.00208 / 0.13 ( 2) link_BETA1-4 : angle 1.62811 / 1.19 ( 6) link_NAG-ASN : bond 0.00734 / 0.45 ( 9) link_NAG-ASN : angle 4.77341 / 3.11 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 226 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.7859 (mmm) cc_final: 0.7375 (mmp) REVERT: A 290 MET cc_start: 0.8748 (mmm) cc_final: 0.8462 (tpt) REVERT: A 409 ASN cc_start: 0.6939 (t0) cc_final: 0.6353 (t0) REVERT: A 835 ARG cc_start: 0.7153 (ptt180) cc_final: 0.6818 (ptm160) REVERT: A 1532 MET cc_start: 0.9223 (mtt) cc_final: 0.8904 (mtp) REVERT: A 1533 MET cc_start: 0.8564 (mtt) cc_final: 0.8345 (mtt) REVERT: A 1593 MET cc_start: 0.6679 (ttm) cc_final: 0.6019 (mmt) REVERT: A 1688 MET cc_start: 0.8353 (mmm) cc_final: 0.7977 (mmm) REVERT: C 71 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6375 (mp0) outliers start: 18 outliers final: 1 residues processed: 236 average time/residue: 0.5574 time to fit residues: 144.3149 Evaluate side-chains 144 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1441 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 278 ASN A 412 ASN A 805 GLN A 809 ASN A1180 ASN A1363 GLN A1378 GLN A1470 GLN A1541 GLN A1753 ASN B 75 ASN C 104 ASN C 131 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.174544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.121711 restraints weight = 62091.622| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.77 r_work: 0.3248 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13937 Z= 0.166 Angle : 0.653 10.425 18832 Z= 0.332 Chirality : 0.045 0.408 2105 Planarity : 0.005 0.061 2186 Dihedral : 20.216 157.508 2365 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.28 % Allowed : 15.39 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.60 (0.21), residues: 1536 helix: 1.39 (0.17), residues: 925 sheet: -0.79 (0.39), residues: 144 loop : -1.17 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 96 TYR 0.022 0.002 TYR A 362 PHE 0.021 0.002 PHE A1440 TRP 0.020 0.002 TRP A1408 HIS 0.007 0.002 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (13915) covalent geometry : angle 0.63744 / 0.33 (18777) SS BOND : bond 0.00435 / 0.28 ( 11) SS BOND : angle 1.08286 / 0.70 ( 22) hydrogen bonds : bond 0.06141 / 4.04 ( 808) hydrogen bonds : angle 4.92718 / 3.42 ( 2328) link_BETA1-4 : bond 0.00767 / 0.45 ( 2) link_BETA1-4 : angle 1.55469 / 1.04 ( 6) link_NAG-ASN : bond 0.00425 / 0.27 ( 9) link_NAG-ASN : angle 3.59308 / 2.49 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.5152 (pp-130) cc_final: 0.4583 (mpt) REVERT: A 249 MET cc_start: 0.7478 (mmm) cc_final: 0.7086 (mmm) REVERT: A 310 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.6970 (pttp) REVERT: A 409 ASN cc_start: 0.6374 (OUTLIER) cc_final: 0.6130 (t0) REVERT: A 798 MET cc_start: 0.5882 (OUTLIER) cc_final: 0.5127 (pp-130) REVERT: A 835 ARG cc_start: 0.7814 (ptt180) cc_final: 0.6441 (ptm160) REVERT: A 842 VAL cc_start: 0.7724 (p) cc_final: 0.7514 (m) REVERT: A 1255 THR cc_start: 0.8192 (m) cc_final: 0.7863 (p) REVERT: A 1504 ILE cc_start: 0.6226 (OUTLIER) cc_final: 0.5931 (pt) REVERT: A 1543 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7895 (tpt) REVERT: A 1593 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.5135 (mmt) REVERT: A 1610 ARG cc_start: 0.8074 (mtm110) cc_final: 0.7846 (mtm110) REVERT: A 1621 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7688 (mt) REVERT: A 1688 MET cc_start: 0.8519 (mmm) cc_final: 0.8087 (mmm) REVERT: B 172 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6751 (mp) REVERT: B 178 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.7056 (tpp) REVERT: C 100 GLU cc_start: 0.6047 (mt-10) cc_final: 0.5834 (mt-10) REVERT: C 113 MET cc_start: 0.5857 (tmm) cc_final: 0.5526 (tmm) outliers start: 45 outliers final: 12 residues processed: 189 average time/residue: 0.4735 time to fit residues: 100.1671 Evaluate side-chains 161 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain A residue 1755 TYR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 148 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 29 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 91 optimal weight: 0.0270 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 chunk 42 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.5040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1378 GLN A1470 GLN A1541 GLN A1732 ASN B 75 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.177545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.143015 restraints weight = 51413.899| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 4.65 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13937 Z= 0.127 Angle : 0.554 9.869 18832 Z= 0.281 Chirality : 0.041 0.356 2105 Planarity : 0.004 0.055 2186 Dihedral : 18.428 160.821 2363 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.06 % Allowed : 16.19 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.40 (0.22), residues: 1536 helix: 2.12 (0.17), residues: 925 sheet: -0.52 (0.40), residues: 144 loop : -1.04 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.019 0.001 TYR A1602 PHE 0.021 0.001 PHE A1440 TRP 0.016 0.001 TRP A1408 HIS 0.006 0.001 HIS A1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (13915) covalent geometry : angle 0.53801 / 0.28 (18777) SS BOND : bond 0.00285 / 0.18 ( 11) SS BOND : angle 1.03283 / 0.67 ( 22) hydrogen bonds : bond 0.05157 / 3.40 ( 808) hydrogen bonds : angle 4.48135 / 3.13 ( 2328) link_BETA1-4 : bond 0.00260 / 0.15 ( 2) link_BETA1-4 : angle 1.47941 / 0.91 ( 6) link_NAG-ASN : bond 0.00389 / 0.26 ( 9) link_NAG-ASN : angle 3.34632 / 2.42 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 SER cc_start: 0.2330 (OUTLIER) cc_final: 0.1689 (t) REVERT: A 147 ASN cc_start: 0.6580 (t0) cc_final: 0.6270 (p0) REVERT: A 217 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6677 (mtm-85) REVERT: A 249 MET cc_start: 0.7949 (mmm) cc_final: 0.7710 (mmm) REVERT: A 409 ASN cc_start: 0.7005 (t0) cc_final: 0.6676 (t0) REVERT: A 742 MET cc_start: 0.2909 (mpp) cc_final: 0.2501 (mtm) REVERT: A 761 MET cc_start: 0.8913 (mtt) cc_final: 0.8659 (mtt) REVERT: A 798 MET cc_start: 0.6006 (OUTLIER) cc_final: 0.5502 (pp-130) REVERT: A 835 ARG cc_start: 0.7817 (ptt180) cc_final: 0.6779 (ptm160) REVERT: A 1593 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.5862 (mmt) REVERT: A 1688 MET cc_start: 0.8348 (mmm) cc_final: 0.7857 (mmt) REVERT: B 178 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7251 (tpp) REVERT: C 142 ILE cc_start: 0.5365 (OUTLIER) cc_final: 0.5163 (mp) outliers start: 42 outliers final: 8 residues processed: 186 average time/residue: 0.4631 time to fit residues: 96.0291 Evaluate side-chains 151 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 142 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 96 optimal weight: 0.2980 chunk 120 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN A 961 ASN A1378 GLN A1470 GLN A1541 GLN B 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.174977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.140046 restraints weight = 52924.170| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 4.86 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13937 Z= 0.135 Angle : 0.552 9.752 18832 Z= 0.280 Chirality : 0.042 0.357 2105 Planarity : 0.004 0.050 2186 Dihedral : 17.180 166.916 2363 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.99 % Allowed : 17.21 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.56 (0.22), residues: 1536 helix: 2.21 (0.17), residues: 934 sheet: -0.45 (0.40), residues: 144 loop : -0.97 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 907 TYR 0.018 0.002 TYR A1602 PHE 0.024 0.001 PHE A 963 TRP 0.008 0.001 TRP A1408 HIS 0.005 0.001 HIS A1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (13915) covalent geometry : angle 0.53767 / 0.28 (18777) SS BOND : bond 0.00535 / 0.31 ( 11) SS BOND : angle 1.04051 / 0.67 ( 22) hydrogen bonds : bond 0.04990 / 3.31 ( 808) hydrogen bonds : angle 4.35430 / 3.04 ( 2328) link_BETA1-4 : bond 0.00366 / 0.22 ( 2) link_BETA1-4 : angle 1.34562 / 0.87 ( 6) link_NAG-ASN : bond 0.00407 / 0.28 ( 9) link_NAG-ASN : angle 3.16067 / 2.26 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 147 ASN cc_start: 0.6611 (t0) cc_final: 0.6295 (p0) REVERT: A 249 MET cc_start: 0.8009 (mmm) cc_final: 0.7803 (mmm) REVERT: A 409 ASN cc_start: 0.6928 (t0) cc_final: 0.6577 (t0) REVERT: A 742 MET cc_start: 0.2960 (mpp) cc_final: 0.2545 (mtm) REVERT: A 759 LEU cc_start: 0.8226 (tt) cc_final: 0.7990 (mp) REVERT: A 761 MET cc_start: 0.9078 (mtt) cc_final: 0.8822 (mtt) REVERT: A 798 MET cc_start: 0.6030 (OUTLIER) cc_final: 0.5567 (pp-130) REVERT: A 835 ARG cc_start: 0.7923 (ptt180) cc_final: 0.6991 (ptm160) REVERT: A 963 PHE cc_start: 0.7151 (m-80) cc_final: 0.6932 (m-80) REVERT: A 1593 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.5639 (mmt) REVERT: A 1688 MET cc_start: 0.8364 (mmm) cc_final: 0.8008 (mmm) REVERT: A 1751 VAL cc_start: 0.8884 (m) cc_final: 0.8626 (t) REVERT: B 66 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6260 (pm20) REVERT: B 154 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6881 (tpt) REVERT: B 171 THR cc_start: 0.8134 (m) cc_final: 0.7860 (m) REVERT: B 172 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7515 (mp) REVERT: B 178 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.7325 (tpp) REVERT: C 56 TYR cc_start: 0.7941 (m-80) cc_final: 0.7735 (m-80) outliers start: 41 outliers final: 12 residues processed: 176 average time/residue: 0.4725 time to fit residues: 92.2582 Evaluate side-chains 153 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 148 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 60 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 127 optimal weight: 0.0670 chunk 82 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 853 ASN A 911 ASN A1378 GLN A1470 GLN A1541 GLN B 79 GLN C 131 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.170178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.116642 restraints weight = 58318.524| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.54 r_work: 0.3184 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13937 Z= 0.143 Angle : 0.563 9.631 18832 Z= 0.284 Chirality : 0.042 0.379 2105 Planarity : 0.004 0.050 2186 Dihedral : 16.458 174.911 2363 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.36 % Allowed : 17.29 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.52 (0.21), residues: 1536 helix: 2.21 (0.17), residues: 932 sheet: -0.85 (0.40), residues: 157 loop : -0.90 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 220 TYR 0.023 0.002 TYR B 32 PHE 0.026 0.002 PHE A 963 TRP 0.006 0.001 TRP A1408 HIS 0.005 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (13915) covalent geometry : angle 0.54863 / 0.28 (18777) SS BOND : bond 0.00247 / 0.18 ( 11) SS BOND : angle 1.12326 / 0.74 ( 22) hydrogen bonds : bond 0.05065 / 3.37 ( 808) hydrogen bonds : angle 4.31141 / 3.01 ( 2328) link_BETA1-4 : bond 0.00266 / 0.15 ( 2) link_BETA1-4 : angle 1.46078 / 0.92 ( 6) link_NAG-ASN : bond 0.00311 / 0.20 ( 9) link_NAG-ASN : angle 3.17241 / 2.28 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.5110 (OUTLIER) cc_final: 0.4846 (tpp) REVERT: A 147 ASN cc_start: 0.6915 (t0) cc_final: 0.6215 (p0) REVERT: A 217 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6174 (mtm-85) REVERT: A 249 MET cc_start: 0.7527 (mmm) cc_final: 0.7125 (mmm) REVERT: A 409 ASN cc_start: 0.6370 (OUTLIER) cc_final: 0.6137 (t0) REVERT: A 742 MET cc_start: 0.2573 (mpp) cc_final: 0.2271 (mtm) REVERT: A 759 LEU cc_start: 0.8279 (tt) cc_final: 0.7864 (mp) REVERT: A 793 LEU cc_start: 0.5161 (OUTLIER) cc_final: 0.4922 (tp) REVERT: A 798 MET cc_start: 0.5848 (OUTLIER) cc_final: 0.5071 (pp-130) REVERT: A 1278 LEU cc_start: 0.7648 (tp) cc_final: 0.7054 (tt) REVERT: A 1487 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6496 (mppt) REVERT: A 1613 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8464 (mmm160) REVERT: A 1751 VAL cc_start: 0.8593 (m) cc_final: 0.8323 (t) REVERT: A 1761 GLU cc_start: 0.7837 (tp30) cc_final: 0.7628 (tp30) REVERT: B 66 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.5928 (pm20) REVERT: B 171 THR cc_start: 0.7333 (m) cc_final: 0.7054 (m) REVERT: B 172 ILE cc_start: 0.7096 (OUTLIER) cc_final: 0.6814 (mp) REVERT: B 178 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.7206 (tpp) REVERT: C 142 ILE cc_start: 0.4168 (OUTLIER) cc_final: 0.3618 (mp) REVERT: C 148 MET cc_start: 0.6182 (OUTLIER) cc_final: 0.5943 (pmm) outliers start: 46 outliers final: 13 residues processed: 178 average time/residue: 0.4764 time to fit residues: 94.2234 Evaluate side-chains 161 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1613 ARG Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 148 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 83 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 24 optimal weight: 0.0470 chunk 66 optimal weight: 0.0370 chunk 22 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 853 ASN A1378 GLN A1470 GLN A1541 GLN B 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.171695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119003 restraints weight = 60935.742| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.37 r_work: 0.3208 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13937 Z= 0.114 Angle : 0.524 9.590 18832 Z= 0.264 Chirality : 0.040 0.335 2105 Planarity : 0.004 0.052 2186 Dihedral : 15.837 178.918 2363 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.14 % Allowed : 17.94 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.70 (0.22), residues: 1536 helix: 2.34 (0.17), residues: 934 sheet: -0.72 (0.40), residues: 157 loop : -0.82 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.021 0.001 TYR A1602 PHE 0.027 0.001 PHE C 80 TRP 0.008 0.001 TRP A1408 HIS 0.004 0.001 HIS A1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (13915) covalent geometry : angle 0.51315 / 0.26 (18777) SS BOND : bond 0.00205 / 0.16 ( 11) SS BOND : angle 0.83939 / 0.56 ( 22) hydrogen bonds : bond 0.04493 / 2.98 ( 808) hydrogen bonds : angle 4.15934 / 2.91 ( 2328) link_BETA1-4 : bond 0.00309 / 0.18 ( 2) link_BETA1-4 : angle 1.29305 / 0.85 ( 6) link_NAG-ASN : bond 0.00339 / 0.22 ( 9) link_NAG-ASN : angle 2.66890 / 1.87 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 SER cc_start: 0.4465 (OUTLIER) cc_final: 0.4067 (t) REVERT: A 147 ASN cc_start: 0.6937 (t0) cc_final: 0.6165 (p0) REVERT: A 249 MET cc_start: 0.7518 (mmm) cc_final: 0.7085 (mmm) REVERT: A 409 ASN cc_start: 0.6305 (OUTLIER) cc_final: 0.6087 (t0) REVERT: A 742 MET cc_start: 0.2426 (mpp) cc_final: 0.2121 (mtm) REVERT: A 759 LEU cc_start: 0.8202 (tt) cc_final: 0.7767 (mp) REVERT: A 798 MET cc_start: 0.5693 (OUTLIER) cc_final: 0.4944 (pp-130) REVERT: A 835 ARG cc_start: 0.7967 (ptt180) cc_final: 0.6774 (ptm160) REVERT: A 1278 LEU cc_start: 0.7700 (tp) cc_final: 0.7104 (tt) REVERT: A 1487 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6576 (mppt) REVERT: A 1593 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6678 (tmm) REVERT: A 1688 MET cc_start: 0.8568 (mmm) cc_final: 0.8251 (mmm) REVERT: A 1751 VAL cc_start: 0.8562 (m) cc_final: 0.8305 (t) REVERT: A 1761 GLU cc_start: 0.7750 (tp30) cc_final: 0.7523 (tp30) REVERT: B 66 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.5969 (pm20) REVERT: B 154 MET cc_start: 0.7205 (OUTLIER) cc_final: 0.6611 (tpt) REVERT: B 171 THR cc_start: 0.7234 (m) cc_final: 0.6943 (m) REVERT: B 178 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.7157 (tpp) REVERT: C 148 MET cc_start: 0.6244 (OUTLIER) cc_final: 0.5998 (pmm) outliers start: 43 outliers final: 17 residues processed: 180 average time/residue: 0.4973 time to fit residues: 99.5049 Evaluate side-chains 167 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 148 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 150 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 115 optimal weight: 0.0270 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 853 ASN A1378 GLN A1470 GLN A1541 GLN B 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.170318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.116740 restraints weight = 63750.164| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.81 r_work: 0.3173 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13937 Z= 0.125 Angle : 0.535 9.674 18832 Z= 0.269 Chirality : 0.041 0.351 2105 Planarity : 0.004 0.053 2186 Dihedral : 15.403 176.205 2363 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.99 % Allowed : 18.23 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.69 (0.22), residues: 1536 helix: 2.33 (0.17), residues: 934 sheet: -0.76 (0.41), residues: 156 loop : -0.82 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 835 TYR 0.021 0.001 TYR A1602 PHE 0.019 0.001 PHE A1440 TRP 0.011 0.001 TRP C 67 HIS 0.004 0.001 HIS A1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (13915) covalent geometry : angle 0.52229 / 0.27 (18777) SS BOND : bond 0.00362 / 0.28 ( 11) SS BOND : angle 0.84268 / 0.58 ( 22) hydrogen bonds : bond 0.04641 / 3.08 ( 808) hydrogen bonds : angle 4.16440 / 2.91 ( 2328) link_BETA1-4 : bond 0.00222 / 0.13 ( 2) link_BETA1-4 : angle 1.36864 / 0.90 ( 6) link_NAG-ASN : bond 0.00312 / 0.20 ( 9) link_NAG-ASN : angle 2.93857 / 2.13 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 SER cc_start: 0.4431 (OUTLIER) cc_final: 0.4043 (t) REVERT: A 147 ASN cc_start: 0.6908 (t0) cc_final: 0.6152 (p0) REVERT: A 217 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6121 (ttm-80) REVERT: A 249 MET cc_start: 0.7522 (mmm) cc_final: 0.7086 (mmm) REVERT: A 409 ASN cc_start: 0.6338 (OUTLIER) cc_final: 0.6120 (t0) REVERT: A 742 MET cc_start: 0.2609 (mpp) cc_final: 0.2280 (mtm) REVERT: A 759 LEU cc_start: 0.8272 (tt) cc_final: 0.7828 (mp) REVERT: A 798 MET cc_start: 0.5709 (OUTLIER) cc_final: 0.4984 (pp-130) REVERT: A 835 ARG cc_start: 0.7965 (ptt180) cc_final: 0.6794 (ptm160) REVERT: A 1278 LEU cc_start: 0.7741 (tp) cc_final: 0.7134 (tt) REVERT: A 1487 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6581 (mppt) REVERT: A 1593 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.6673 (tmm) REVERT: A 1613 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8505 (mmm160) REVERT: A 1688 MET cc_start: 0.8583 (mmm) cc_final: 0.8280 (mmm) REVERT: A 1751 VAL cc_start: 0.8558 (m) cc_final: 0.8299 (t) REVERT: A 1761 GLU cc_start: 0.7720 (tp30) cc_final: 0.7386 (tp30) REVERT: B 66 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.6003 (pm20) REVERT: B 154 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6629 (tpt) REVERT: B 171 THR cc_start: 0.7225 (m) cc_final: 0.6952 (m) REVERT: B 172 ILE cc_start: 0.7066 (OUTLIER) cc_final: 0.6807 (mp) REVERT: B 178 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7074 (tpp) REVERT: C 130 MET cc_start: 0.6759 (tpt) cc_final: 0.6472 (mmm) outliers start: 41 outliers final: 17 residues processed: 168 average time/residue: 0.5144 time to fit residues: 95.9344 Evaluate side-chains 167 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain A residue 1613 ARG Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 71 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 66 optimal weight: 0.0870 chunk 15 optimal weight: 8.9990 chunk 130 optimal weight: 0.1980 chunk 97 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 36 optimal weight: 0.0980 overall best weight: 0.4360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 853 ASN A1378 GLN A1470 GLN A1541 GLN B 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.171922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131477 restraints weight = 49527.435| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 5.93 r_work: 0.3148 rms_B_bonded: 5.09 restraints_weight: 2.0000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13937 Z= 0.108 Angle : 0.510 9.563 18832 Z= 0.258 Chirality : 0.040 0.314 2105 Planarity : 0.004 0.054 2186 Dihedral : 14.979 172.026 2363 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.55 % Allowed : 18.67 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.90 (0.22), residues: 1536 helix: 2.49 (0.17), residues: 928 sheet: -0.32 (0.42), residues: 146 loop : -0.79 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 835 TYR 0.023 0.001 TYR A1602 PHE 0.046 0.001 PHE A 112 TRP 0.008 0.001 TRP A1408 HIS 0.004 0.001 HIS A1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (13915) covalent geometry : angle 0.49991 / 0.26 (18777) SS BOND : bond 0.00213 / 0.16 ( 11) SS BOND : angle 0.71883 / 0.48 ( 22) hydrogen bonds : bond 0.04238 / 2.81 ( 808) hydrogen bonds : angle 4.07968 / 2.84 ( 2328) link_BETA1-4 : bond 0.00290 / 0.17 ( 2) link_BETA1-4 : angle 1.25092 / 0.84 ( 6) link_NAG-ASN : bond 0.00315 / 0.21 ( 9) link_NAG-ASN : angle 2.61147 / 1.81 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 SER cc_start: 0.4442 (OUTLIER) cc_final: 0.4054 (t) REVERT: A 133 MET cc_start: 0.5736 (tpp) cc_final: 0.5427 (tpp) REVERT: A 147 ASN cc_start: 0.6988 (t0) cc_final: 0.6170 (p0) REVERT: A 217 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.5978 (ttm-80) REVERT: A 249 MET cc_start: 0.7693 (mmm) cc_final: 0.7293 (mmm) REVERT: A 409 ASN cc_start: 0.6267 (OUTLIER) cc_final: 0.6053 (t0) REVERT: A 742 MET cc_start: 0.2592 (mpp) cc_final: 0.2252 (mtm) REVERT: A 759 LEU cc_start: 0.8300 (tt) cc_final: 0.7859 (mp) REVERT: A 798 MET cc_start: 0.6031 (OUTLIER) cc_final: 0.5277 (pp-130) REVERT: A 835 ARG cc_start: 0.8018 (ptt180) cc_final: 0.6787 (ptm160) REVERT: A 870 MET cc_start: 0.8116 (tpp) cc_final: 0.7874 (mmm) REVERT: A 963 PHE cc_start: 0.7273 (m-10) cc_final: 0.7034 (m-80) REVERT: A 1278 LEU cc_start: 0.7755 (tp) cc_final: 0.7150 (tt) REVERT: A 1470 GLN cc_start: 0.8013 (mt0) cc_final: 0.7698 (mm110) REVERT: A 1487 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.6727 (mppt) REVERT: A 1593 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6721 (tmm) REVERT: A 1613 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8441 (mmm160) REVERT: A 1688 MET cc_start: 0.8675 (mmm) cc_final: 0.8406 (mmm) REVERT: A 1751 VAL cc_start: 0.8599 (m) cc_final: 0.8351 (t) REVERT: A 1761 GLU cc_start: 0.7874 (tp30) cc_final: 0.7627 (tp30) REVERT: B 39 LEU cc_start: 0.8709 (mt) cc_final: 0.8497 (mp) REVERT: B 66 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6172 (pm20) REVERT: B 154 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6671 (tpt) REVERT: B 171 THR cc_start: 0.7280 (m) cc_final: 0.6974 (m) REVERT: B 172 ILE cc_start: 0.7183 (OUTLIER) cc_final: 0.6941 (mp) REVERT: B 178 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7371 (tpp) outliers start: 35 outliers final: 13 residues processed: 172 average time/residue: 0.4725 time to fit residues: 90.3000 Evaluate side-chains 167 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 901 ASP Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain A residue 1613 ARG Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 71 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 47 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 853 ASN A1378 GLN B 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.166762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.126481 restraints weight = 52009.294| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 6.02 r_work: 0.3051 rms_B_bonded: 5.33 restraints_weight: 2.0000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13937 Z= 0.208 Angle : 0.620 10.022 18832 Z= 0.311 Chirality : 0.044 0.437 2105 Planarity : 0.005 0.055 2186 Dihedral : 15.319 166.439 2363 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.77 % Allowed : 18.67 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.45 (0.21), residues: 1536 helix: 2.13 (0.17), residues: 926 sheet: -0.61 (0.41), residues: 146 loop : -0.94 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 94 TYR 0.025 0.002 TYR A1602 PHE 0.032 0.002 PHE A 112 TRP 0.012 0.002 TRP A1178 HIS 0.006 0.002 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 (13915) covalent geometry : angle 0.60736 / 0.31 (18777) SS BOND : bond 0.00261 / 0.20 ( 11) SS BOND : angle 1.11907 / 0.72 ( 22) hydrogen bonds : bond 0.05580 / 3.71 ( 808) hydrogen bonds : angle 4.34708 / 3.03 ( 2328) link_BETA1-4 : bond 0.00133 / 0.08 ( 2) link_BETA1-4 : angle 1.79809 / 1.12 ( 6) link_NAG-ASN : bond 0.00290 / 0.19 ( 9) link_NAG-ASN : angle 3.15698 / 2.14 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 SER cc_start: 0.4295 (OUTLIER) cc_final: 0.4042 (t) REVERT: A 147 ASN cc_start: 0.7101 (t0) cc_final: 0.6313 (p0) REVERT: A 217 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6051 (ttm-80) REVERT: A 249 MET cc_start: 0.7698 (mmm) cc_final: 0.7276 (mmm) REVERT: A 409 ASN cc_start: 0.6320 (OUTLIER) cc_final: 0.6089 (t0) REVERT: A 742 MET cc_start: 0.3086 (mpp) cc_final: 0.2447 (ptt) REVERT: A 759 LEU cc_start: 0.8251 (tt) cc_final: 0.7815 (mp) REVERT: A 798 MET cc_start: 0.6158 (ppp) cc_final: 0.5430 (pp-130) REVERT: A 1470 GLN cc_start: 0.7965 (mt0) cc_final: 0.7620 (mm110) REVERT: A 1487 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.7110 (mtpt) REVERT: A 1495 LYS cc_start: 0.7530 (ptpp) cc_final: 0.6985 (tttp) REVERT: A 1593 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6738 (tmm) REVERT: A 1613 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8513 (mmm160) REVERT: A 1688 MET cc_start: 0.8705 (mmm) cc_final: 0.8392 (mmm) REVERT: A 1751 VAL cc_start: 0.8675 (m) cc_final: 0.8397 (t) REVERT: A 1761 GLU cc_start: 0.7889 (tp30) cc_final: 0.7583 (tp30) REVERT: B 66 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.6105 (pm20) REVERT: B 154 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.6823 (tpt) REVERT: B 171 THR cc_start: 0.7379 (m) cc_final: 0.7123 (m) REVERT: B 172 ILE cc_start: 0.7195 (OUTLIER) cc_final: 0.6941 (mp) REVERT: B 178 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7210 (tpp) REVERT: C 50 CYS cc_start: 0.5824 (t) cc_final: 0.5098 (t) REVERT: C 130 MET cc_start: 0.6870 (tpt) cc_final: 0.6526 (mmm) outliers start: 38 outliers final: 16 residues processed: 171 average time/residue: 0.5076 time to fit residues: 96.2020 Evaluate side-chains 168 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain A residue 1613 ARG Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 142 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 28 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 chunk 6 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 chunk 1 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 853 ASN A1378 GLN A1541 GLN B 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.169807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.128555 restraints weight = 43738.600| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 5.24 r_work: 0.3128 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13937 Z= 0.119 Angle : 0.539 9.563 18832 Z= 0.272 Chirality : 0.040 0.354 2105 Planarity : 0.004 0.057 2186 Dihedral : 14.839 161.731 2363 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.04 % Allowed : 19.33 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.70 (0.21), residues: 1536 helix: 2.35 (0.17), residues: 926 sheet: -0.46 (0.42), residues: 146 loop : -0.91 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1499 TYR 0.025 0.001 TYR A1602 PHE 0.044 0.001 PHE A 112 TRP 0.011 0.001 TRP A1245 HIS 0.003 0.001 HIS A1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (13915) covalent geometry : angle 0.52842 / 0.27 (18777) SS BOND : bond 0.00189 / 0.14 ( 11) SS BOND : angle 0.77347 / 0.51 ( 22) hydrogen bonds : bond 0.04562 / 3.02 ( 808) hydrogen bonds : angle 4.15548 / 2.90 ( 2328) link_BETA1-4 : bond 0.00235 / 0.14 ( 2) link_BETA1-4 : angle 1.37410 / 0.90 ( 6) link_NAG-ASN : bond 0.00312 / 0.20 ( 9) link_NAG-ASN : angle 2.70130 / 1.85 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 SER cc_start: 0.4243 (OUTLIER) cc_final: 0.3942 (t) REVERT: A 147 ASN cc_start: 0.7079 (t0) cc_final: 0.6287 (p0) REVERT: A 217 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.5906 (ttm-80) REVERT: A 249 MET cc_start: 0.7640 (mmm) cc_final: 0.7248 (mmm) REVERT: A 409 ASN cc_start: 0.6300 (OUTLIER) cc_final: 0.6082 (t0) REVERT: A 742 MET cc_start: 0.2802 (mpp) cc_final: 0.2459 (mtm) REVERT: A 759 LEU cc_start: 0.8231 (tt) cc_final: 0.7797 (mp) REVERT: A 798 MET cc_start: 0.6183 (ppp) cc_final: 0.5388 (pp-130) REVERT: A 835 ARG cc_start: 0.8041 (ptt180) cc_final: 0.6740 (ptm160) REVERT: A 1470 GLN cc_start: 0.7953 (mt0) cc_final: 0.7621 (mm110) REVERT: A 1487 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6687 (mppt) REVERT: A 1495 LYS cc_start: 0.7588 (ptpp) cc_final: 0.7079 (tttp) REVERT: A 1593 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6679 (tmm) REVERT: A 1613 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8505 (mmm160) REVERT: A 1688 MET cc_start: 0.8660 (mmm) cc_final: 0.8371 (mmm) REVERT: A 1751 VAL cc_start: 0.8612 (m) cc_final: 0.8347 (t) REVERT: A 1761 GLU cc_start: 0.7811 (tp30) cc_final: 0.7574 (tp30) REVERT: B 66 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.6095 (pm20) REVERT: B 154 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6676 (tpt) REVERT: B 171 THR cc_start: 0.7252 (m) cc_final: 0.6959 (m) REVERT: B 172 ILE cc_start: 0.7116 (OUTLIER) cc_final: 0.6872 (mp) REVERT: B 178 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.7220 (tpp) REVERT: C 50 CYS cc_start: 0.5764 (t) cc_final: 0.5084 (t) outliers start: 28 outliers final: 14 residues processed: 165 average time/residue: 0.5100 time to fit residues: 93.4817 Evaluate side-chains 167 residues out of total 1397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain A residue 845 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1487 LYS Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain A residue 1613 ARG Chi-restraints excluded: chain A residue 1621 LEU Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 178 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 53 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 85 optimal weight: 0.2980 chunk 115 optimal weight: 1.9990 chunk 122 optimal weight: 0.0020 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 853 ASN A1378 GLN A1502 ASN A1541 GLN B 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.169179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.128854 restraints weight = 49468.691| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 5.72 r_work: 0.3097 rms_B_bonded: 5.27 restraints_weight: 2.0000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13937 Z= 0.127 Angle : 0.545 9.623 18832 Z= 0.274 Chirality : 0.041 0.362 2105 Planarity : 0.004 0.056 2186 Dihedral : 14.512 158.626 2363 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.26 % Allowed : 19.26 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.74 (0.21), residues: 1536 helix: 2.38 (0.17), residues: 926 sheet: -0.39 (0.42), residues: 146 loop : -0.90 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 117 TYR 0.024 0.001 TYR A1602 PHE 0.018 0.001 PHE A1440 TRP 0.008 0.001 TRP A1408 HIS 0.003 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (13915) covalent geometry : angle 0.53464 / 0.27 (18777) SS BOND : bond 0.00199 / 0.15 ( 11) SS BOND : angle 0.81472 / 0.54 ( 22) hydrogen bonds : bond 0.04623 / 3.07 ( 808) hydrogen bonds : angle 4.11510 / 2.87 ( 2328) link_BETA1-4 : bond 0.00215 / 0.13 ( 2) link_BETA1-4 : angle 1.40889 / 0.95 ( 6) link_NAG-ASN : bond 0.00283 / 0.18 ( 9) link_NAG-ASN : angle 2.71075 / 1.84 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4728.41 seconds wall clock time: 81 minutes 23.75 seconds (4883.75 seconds total)