Starting phenix.real_space_refine on Thu Jul 2 20:28:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k18_22621/07_2026/7k18_22621.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k18_22621/07_2026/7k18_22621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k18_22621/07_2026/7k18_22621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k18_22621/07_2026/7k18_22621.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7k18_22621/07_2026/7k18_22621.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k18_22621/07_2026/7k18_22621.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k18_22621/07_2026/7k18_22621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k18_22621/07_2026/7k18_22621.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 5 5.49 5 S 76 5.16 5 C 6442 2.51 5 N 1511 2.21 5 O 1715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 9749 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1128, 8861 Classifications: {'peptide': 1128} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 1096} Chain breaks: 5 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'HIS:plan': 1, 'PHE:plan': 5, 'ARG:plan': 3, 'GLU:plan': 7, 'TYR:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 119 Chain: "B" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 489 Classifications: {'peptide': 67} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 62} Chain: "C" 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: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 304 Unusual residues: {'6OU': 11, 'NAG': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 276 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'6OU:plan-1': 9, '6OU:plan-3': 1, '6OU:plan-2': 2} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 1.50, per 1000 atoms: 0.15 Number of scatterers: 9749 At special positions: 0 Unit cell: (133.056, 125.664, 107.712, 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 76 16.00 P 5 15.00 O 1715 8.00 N 1511 7.00 C 6442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 336 " distance=1.81 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 342 " distance=2.03 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 918 " distance=2.80 Simple disulfide: pdb=" SG CYS A1365 " - pdb=" SG CYS A1386 " distance=2.74 Simple disulfide: pdb=" SG CYS A1730 " - pdb=" SG CYS A1744 " distance=2.03 Simple disulfide: pdb=" SG CYS B 12 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 37 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 47 " distance=2.32 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 49 " distance=1.41 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=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2201 " - " ASN A 319 " " NAG C 1 " - " ASN A1382 " " NAG D 1 " - " ASN A 329 " " NAG E 1 " - " ASN A1390 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 214.3 milliseconds 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2236 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 2 sheets defined 73.7% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'A' and resid 132 through 150 removed outlier: 3.536A pdb=" N MET A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 160 through 181 Processing helix chain 'A' and resid 183 through 190 Processing helix chain 'A' and resid 194 through 211 removed outlier: 3.674A pdb=" N ASP A 198 " --> pdb=" O TRP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 227 removed outlier: 3.542A pdb=" N ARG A 223 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.629A pdb=" N SER A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 251 removed outlier: 3.959A pdb=" N LYS A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 274 Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 312 through 315 Processing helix chain 'A' and resid 358 through 372 removed outlier: 3.718A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.704A pdb=" N LEU A 378 " --> pdb=" O CYS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 390 through 401 Processing helix chain 'A' and resid 401 through 423 Processing helix chain 'A' and resid 700 through 716 Processing helix chain 'A' and resid 720 through 737 removed outlier: 3.544A pdb=" N LEU A 737 " --> pdb=" O LEU A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 772 Processing helix chain 'A' and resid 775 through 780 Processing helix chain 'A' and resid 780 through 797 Processing helix chain 'A' and resid 808 through 822 removed outlier: 3.911A pdb=" N PHE A 811 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A 813 " --> pdb=" O SER A 810 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A 818 " --> pdb=" O ARG A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 836 Processing helix chain 'A' and resid 840 through 869 removed outlier: 5.081A pdb=" N LYS A 864 " --> pdb=" O GLN A 860 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ASN A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 873 Processing helix chain 'A' and resid 886 through 900 removed outlier: 3.599A pdb=" N ALA A 890 " --> pdb=" O ASP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 913 removed outlier: 4.158A pdb=" N ASP A 908 " --> pdb=" O GLU A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 945 removed outlier: 3.637A pdb=" N PHE A 945 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1205 Processing helix chain 'A' and resid 1206 through 1226 Processing helix chain 'A' and resid 1234 through 1270 removed outlier: 3.737A pdb=" N LYS A1238 " --> pdb=" O ARG A1234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A1239 " --> pdb=" O LYS A1235 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N PHE A1265 " --> pdb=" O VAL A1261 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N LYS A1266 " --> pdb=" O ALA A1262 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS A1267 " --> pdb=" O TYR A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1293 Processing helix chain 'A' and resid 1301 through 1306 Processing helix chain 'A' and resid 1307 through 1318 Proline residue: A1312 - end of helix removed outlier: 3.698A pdb=" N LEU A1316 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1331 removed outlier: 3.677A pdb=" N VAL A1324 " --> pdb=" O GLU A1320 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1359 removed outlier: 4.304A pdb=" N ASN A1338 " --> pdb=" O PRO A1334 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL A1339 " --> pdb=" O SER A1335 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A1350 " --> pdb=" O PHE A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1387 Processing helix chain 'A' and resid 1388 through 1390 No H-bonds generated for 'chain 'A' and resid 1388 through 1390' Processing helix chain 'A' and resid 1407 through 1419 Processing helix chain 'A' and resid 1422 through 1432 removed outlier: 3.783A pdb=" N ILE A1426 " --> pdb=" O GLY A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1447 No H-bonds generated for 'chain 'A' and resid 1445 through 1447' Processing helix chain 'A' and resid 1448 through 1462 removed outlier: 3.788A pdb=" N PHE A1452 " --> pdb=" O MET A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1482 removed outlier: 3.816A pdb=" N LYS A1480 " --> pdb=" O ASN A1476 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1504 Processing helix chain 'A' and resid 1517 through 1528 Processing helix chain 'A' and resid 1529 through 1547 removed outlier: 3.878A pdb=" N ASP A1533 " --> pdb=" O LYS A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1582 Processing helix chain 'A' and resid 1585 through 1589 removed outlier: 4.364A pdb=" N TYR A1588 " --> pdb=" O ARG A1585 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1614 removed outlier: 4.034A pdb=" N THR A1608 " --> pdb=" O SER A1604 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N VAL A1609 " --> pdb=" O ILE A1605 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A1610 " --> pdb=" O VAL A1606 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE A1613 " --> pdb=" O VAL A1609 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1630 removed outlier: 3.596A pdb=" N ILE A1627 " --> pdb=" O PHE A1624 " (cutoff:3.500A) Processing helix chain 'A' and resid 1631 through 1639 removed outlier: 4.204A pdb=" N ILE A1635 " --> pdb=" O ARG A1631 " (cutoff:3.500A) Processing helix chain 'A' and resid 1643 through 1681 removed outlier: 3.605A pdb=" N THR A1647 " --> pdb=" O LYS A1643 " (cutoff:3.500A) Proline residue: A1657 - end of helix Processing helix chain 'A' and resid 1698 through 1711 removed outlier: 3.974A pdb=" N THR A1711 " --> pdb=" O PHE A1707 " (cutoff:3.500A) Processing helix chain 'A' and resid 1714 through 1724 Proline residue: A1721 - end of helix removed outlier: 3.987A pdb=" N ASN A1724 " --> pdb=" O SER A1720 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1779 Processing helix chain 'B' and resid 23 through 31 Processing sheet with id=AA1, first strand: chain 'A' and resid 280 through 282 Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.569A pdb=" N LEU B 52 " --> pdb=" O ARG B 2 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLY B 4 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ASN B 50 " --> pdb=" O GLY B 4 " (cutoff:3.500A) 622 hydrogen bonds defined for protein. 1767 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: 1.01 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1473 1.31 - 1.44: 2779 1.44 - 1.56: 5577 1.56 - 1.69: 13 1.69 - 1.82: 119 Bond restraints: 9961 Sorted by residual: bond pdb=" C07 6OU A2212 " pdb=" C08 6OU A2212 " ideal model delta sigma weight residual 1.524 1.313 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C07 6OU A2211 " pdb=" C08 6OU A2211 " ideal model delta sigma weight residual 1.524 1.318 0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" N PRO A1374 " pdb=" CD PRO A1374 " ideal model delta sigma weight residual 1.473 1.585 -0.112 1.40e-02 5.10e+03 6.35e+01 bond pdb=" N PRO A1732 " pdb=" CD PRO A1732 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.84e+01 bond pdb=" C16 6OU A2202 " pdb=" O18 6OU A2202 " ideal model delta sigma weight residual 1.327 1.401 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 9956 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 13150 3.21 - 6.42: 249 6.42 - 9.63: 47 9.63 - 12.85: 9 12.85 - 16.06: 6 Bond angle restraints: 13461 Sorted by residual: angle pdb=" N LYS A1302 " pdb=" CA LYS A1302 " pdb=" C LYS A1302 " ideal model delta sigma weight residual 113.12 102.04 11.08 1.25e+00 6.40e-01 7.85e+01 angle pdb=" N ILE A1366 " pdb=" CA ILE A1366 " pdb=" C ILE A1366 " ideal model delta sigma weight residual 108.58 120.32 -11.74 1.44e+00 4.82e-01 6.64e+01 angle pdb=" N CYS A1365 " pdb=" CA CYS A1365 " pdb=" C CYS A1365 " ideal model delta sigma weight residual 108.24 122.39 -14.15 1.81e+00 3.05e-01 6.11e+01 angle pdb=" C CYS A1365 " pdb=" CA CYS A1365 " pdb=" CB CYS A1365 " ideal model delta sigma weight residual 112.05 101.56 10.49 1.52e+00 4.33e-01 4.76e+01 angle pdb=" N ILE A1366 " pdb=" CA ILE A1366 " pdb=" CB ILE A1366 " ideal model delta sigma weight residual 110.72 103.66 7.06 1.09e+00 8.42e-01 4.20e+01 ... (remaining 13456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.14: 5485 33.14 - 66.29: 251 66.29 - 99.43: 14 99.43 - 132.57: 3 132.57 - 165.72: 4 Dihedral angle restraints: 5757 sinusoidal: 2292 harmonic: 3465 Sorted by residual: dihedral pdb=" CB CYS A1730 " pdb=" SG CYS A1730 " pdb=" SG CYS A1744 " pdb=" CB CYS A1744 " ideal model delta sinusoidal sigma weight residual -86.00 -157.61 71.61 1 1.00e+01 1.00e-02 6.57e+01 dihedral pdb=" CB CYS A1365 " pdb=" SG CYS A1365 " pdb=" SG CYS A1386 " pdb=" CB CYS A1386 " ideal model delta sinusoidal sigma weight residual -86.00 -17.68 -68.32 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CB CYS B 16 " pdb=" SG CYS B 16 " pdb=" SG CYS B 37 " pdb=" CB CYS B 37 " ideal model delta sinusoidal sigma weight residual -86.00 -142.04 56.04 1 1.00e+01 1.00e-02 4.24e+01 ... (remaining 5754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1495 0.093 - 0.185: 55 0.185 - 0.278: 6 0.278 - 0.371: 5 0.371 - 0.464: 1 Chirality restraints: 1562 Sorted by residual: chirality pdb=" CA ILE A1301 " pdb=" N ILE A1301 " pdb=" C ILE A1301 " pdb=" CB ILE A1301 " both_signs ideal model delta sigma weight residual False 2.43 2.90 -0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" CA GLU B 29 " pdb=" N GLU B 29 " pdb=" C GLU B 29 " pdb=" CB GLU B 29 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 329 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.74 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 1559 not shown) Planarity restraints: 1634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 319 " -0.077 2.00e-02 2.50e+03 2.41e-01 7.28e+02 pdb=" CG ASN A 319 " -0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN A 319 " 0.246 2.00e-02 2.50e+03 pdb=" ND2 ASN A 319 " -0.383 2.00e-02 2.50e+03 pdb=" C1 NAG A2201 " 0.273 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " -0.083 2.00e-02 2.50e+03 1.63e-01 3.34e+02 pdb=" CG ASN A 329 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " -0.080 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " 0.295 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A1731 " 0.072 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO A1732 " -0.191 5.00e-02 4.00e+02 pdb=" CA PRO A1732 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO A1732 " 0.055 5.00e-02 4.00e+02 ... (remaining 1631 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 92 2.53 - 3.12: 8067 3.12 - 3.71: 15218 3.71 - 4.31: 20984 4.31 - 4.90: 33877 Nonbonded interactions: 78238 Sorted by model distance: nonbonded pdb=" O CYS B 27 " pdb=" N GLY B 32 " model vdw 1.936 3.120 nonbonded pdb=" OD1 ASN A 329 " pdb=" O7 NAG D 1 " model vdw 1.953 3.040 nonbonded pdb=" O LEU A1752 " pdb=" OG1 THR A1756 " model vdw 2.050 3.040 nonbonded pdb=" O LEU A1344 " pdb=" OH TYR A1411 " model vdw 2.071 3.040 nonbonded pdb=" O LEU A 270 " pdb=" CG MET A 274 " model vdw 2.094 3.440 ... (remaining 78233 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 'C' 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=1.00 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: 0.930 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.120 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 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 0.771 9979 Z= 0.733 Angle : 1.337 39.290 13503 Z= 0.631 Chirality : 0.049 0.464 1562 Planarity : 0.006 0.110 1630 Dihedral : 18.249 165.717 3494 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.87 % Favored : 91.79 % Rotamer: Outliers : 3.41 % Allowed : 21.08 % Favored : 75.50 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.17 % 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: -3.42 (0.21), residues: 1181 helix: -1.78 (0.15), residues: 799 sheet: -3.29 (1.22), residues: 14 loop : -3.05 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1308 TYR 0.015 0.002 TYR A 379 PHE 0.013 0.001 PHE A1694 TRP 0.017 0.001 TRP A1715 HIS 0.006 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.33 ( 9961) covalent geometry : angle 1.09438 / 0.53 (13461) SS BOND : bond 0.42408 / 24.00 ( 9) SS BOND : angle 18.24794 / 12.62 ( 18) hydrogen bonds : bond 0.10761 / 6.99 ( 622) hydrogen bonds : angle 6.29344 / 4.53 ( 1767) Misc. bond : bond 0.00305 / 0.16 ( 1) link_BETA1-4 : bond 0.00760 / 0.40 ( 4) link_BETA1-4 : angle 4.46076 / 2.50 ( 12) link_NAG-ASN : bond 0.14302 / 7.38 ( 4) link_NAG-ASN : angle 12.14944 / 6.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 286 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.7867 (mmmt) cc_final: 0.7640 (ttpt) REVERT: A 177 ILE cc_start: 0.7823 (mt) cc_final: 0.7285 (tp) REVERT: A 199 PHE cc_start: 0.7463 (t80) cc_final: 0.7168 (t80) REVERT: A 219 LEU cc_start: 0.6530 (pt) cc_final: 0.6140 (tp) REVERT: A 341 ARG cc_start: 0.7987 (ptm160) cc_final: 0.7369 (mmm-85) REVERT: A 705 MET cc_start: 0.4544 (mmp) cc_final: 0.4128 (tpp) REVERT: A 754 ASN cc_start: 0.6963 (m-40) cc_final: 0.5650 (m-40) REVERT: A 783 ASN cc_start: 0.8057 (m110) cc_final: 0.7825 (m-40) REVERT: A 1298 MET cc_start: 0.2243 (OUTLIER) cc_final: 0.1059 (ptm) REVERT: A 1337 MET cc_start: 0.6682 (mmm) cc_final: 0.6115 (mmm) REVERT: A 1438 GLU cc_start: 0.5554 (pt0) cc_final: 0.5230 (tt0) REVERT: B 15 HIS cc_start: 0.5127 (m90) cc_final: 0.4641 (p-80) outliers start: 34 outliers final: 19 residues processed: 315 average time/residue: 0.0764 time to fit residues: 34.4120 Evaluate side-chains 251 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 231 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 1298 MET Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1494 LYS Chi-restraints excluded: chain A residue 1546 THR Chi-restraints excluded: chain A residue 1551 THR Chi-restraints excluded: chain A residue 1608 THR Chi-restraints excluded: chain A residue 1612 ASP Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1708 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.0070 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN A 151 GLN A 195 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN A 865 ASN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN A1206 HIS ** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.186720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.136770 restraints weight = 14621.127| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.44 r_work: 0.3629 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9979 Z= 0.152 Angle : 0.692 9.496 13503 Z= 0.353 Chirality : 0.042 0.273 1562 Planarity : 0.005 0.069 1630 Dihedral : 14.849 158.844 1483 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.82 % Allowed : 24.10 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.17 % 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: -1.71 (0.23), residues: 1181 helix: -0.44 (0.17), residues: 807 sheet: None (None), residues: 0 loop : -2.55 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1625 TYR 0.029 0.002 TYR A 379 PHE 0.018 0.002 PHE A1596 TRP 0.014 0.001 TRP A1715 HIS 0.003 0.001 HIS B 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 9961) covalent geometry : angle 0.66837 / 0.35 (13461) SS BOND : bond 0.00799 / 0.40 ( 9) SS BOND : angle 3.04801 / 1.71 ( 18) hydrogen bonds : bond 0.04375 / 2.93 ( 622) hydrogen bonds : angle 5.31114 / 3.81 ( 1767) Misc. bond : bond 0.00019 / 0.01 ( 1) link_BETA1-4 : bond 0.00752 / 0.37 ( 4) link_BETA1-4 : angle 2.90176 / 1.65 ( 12) link_NAG-ASN : bond 0.00650 / 0.31 ( 4) link_NAG-ASN : angle 4.01610 / 2.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 254 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8504 (mmmt) cc_final: 0.7810 (ttpt) REVERT: A 177 ILE cc_start: 0.8239 (mt) cc_final: 0.7681 (tp) REVERT: A 199 PHE cc_start: 0.8283 (t80) cc_final: 0.8071 (t80) REVERT: A 206 TYR cc_start: 0.7978 (m-80) cc_final: 0.7757 (m-80) REVERT: A 219 LEU cc_start: 0.7602 (pt) cc_final: 0.6949 (tp) REVERT: A 223 ARG cc_start: 0.7433 (mmm-85) cc_final: 0.6766 (ttm-80) REVERT: A 226 ARG cc_start: 0.7838 (mtt180) cc_final: 0.7534 (mtt-85) REVERT: A 341 ARG cc_start: 0.8511 (ptm160) cc_final: 0.7264 (mmm-85) REVERT: A 705 MET cc_start: 0.5309 (mmp) cc_final: 0.4246 (tpp) REVERT: A 750 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7762 (mt) REVERT: A 817 PHE cc_start: 0.7936 (m-80) cc_final: 0.7603 (m-80) REVERT: A 1193 TRP cc_start: 0.7259 (t-100) cc_final: 0.6893 (t-100) REVERT: A 1197 ARG cc_start: 0.6669 (ttp80) cc_final: 0.6466 (mtp-110) REVERT: A 1234 ARG cc_start: 0.7083 (ptp-170) cc_final: 0.6863 (ptp-170) REVERT: A 1241 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7959 (mm) REVERT: A 1298 MET cc_start: 0.2798 (ttm) cc_final: 0.0945 (ptm) REVERT: A 1337 MET cc_start: 0.7822 (mmm) cc_final: 0.7261 (mmm) REVERT: A 1438 GLU cc_start: 0.6175 (pt0) cc_final: 0.5673 (tt0) REVERT: A 1441 GLN cc_start: 0.4133 (mp10) cc_final: 0.3679 (mp10) REVERT: A 1493 GLN cc_start: 0.6845 (mm-40) cc_final: 0.6382 (mp10) REVERT: A 1618 PHE cc_start: 0.5749 (OUTLIER) cc_final: 0.5393 (m-80) outliers start: 48 outliers final: 27 residues processed: 287 average time/residue: 0.0697 time to fit residues: 29.2508 Evaluate side-chains 252 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 751 GLN Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1609 VAL Chi-restraints excluded: chain A residue 1612 ASP Chi-restraints excluded: chain A residue 1618 PHE Chi-restraints excluded: chain A residue 1667 PHE Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1708 GLN Chi-restraints excluded: chain B residue 48 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A 751 GLN A 754 ASN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.186680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.137596 restraints weight = 14507.803| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.40 r_work: 0.3679 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9979 Z= 0.153 Angle : 0.662 9.653 13503 Z= 0.335 Chirality : 0.041 0.211 1562 Planarity : 0.004 0.059 1630 Dihedral : 13.462 146.727 1462 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 5.42 % Allowed : 25.50 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.24), residues: 1181 helix: 0.16 (0.17), residues: 804 sheet: -3.72 (1.36), residues: 14 loop : -2.37 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1631 TYR 0.027 0.002 TYR A 777 PHE 0.027 0.002 PHE A1753 TRP 0.013 0.001 TRP A1260 HIS 0.003 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 9961) covalent geometry : angle 0.64369 / 0.33 (13461) SS BOND : bond 0.00812 / 0.57 ( 9) SS BOND : angle 2.13172 / 1.22 ( 18) hydrogen bonds : bond 0.04051 / 2.69 ( 622) hydrogen bonds : angle 5.14055 / 3.70 ( 1767) Misc. bond : bond 0.00035 / 0.02 ( 1) link_BETA1-4 : bond 0.00782 / 0.40 ( 4) link_BETA1-4 : angle 2.91765 / 1.68 ( 12) link_NAG-ASN : bond 0.00701 / 0.34 ( 4) link_NAG-ASN : angle 3.64075 / 2.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 239 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8599 (mmmt) cc_final: 0.7908 (ttpt) REVERT: A 223 ARG cc_start: 0.7332 (mmm-85) cc_final: 0.6900 (ttm-80) REVERT: A 226 ARG cc_start: 0.7909 (mtt180) cc_final: 0.7685 (mtt-85) REVERT: A 341 ARG cc_start: 0.8416 (ptm160) cc_final: 0.7187 (mpt180) REVERT: A 705 MET cc_start: 0.5362 (mmp) cc_final: 0.4360 (tpp) REVERT: A 754 ASN cc_start: 0.8030 (m110) cc_final: 0.7619 (m-40) REVERT: A 795 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7280 (tmm) REVERT: A 817 PHE cc_start: 0.8082 (m-80) cc_final: 0.7770 (m-80) REVERT: A 1193 TRP cc_start: 0.7228 (t-100) cc_final: 0.6919 (t-100) REVERT: A 1234 ARG cc_start: 0.7196 (ptp-170) cc_final: 0.6861 (ptp-170) REVERT: A 1241 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7947 (mm) REVERT: A 1298 MET cc_start: 0.2828 (OUTLIER) cc_final: 0.0950 (ptm) REVERT: A 1337 MET cc_start: 0.7902 (mmm) cc_final: 0.7354 (mmm) REVERT: A 1396 TYR cc_start: 0.8305 (m-80) cc_final: 0.8098 (m-80) REVERT: A 1438 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.4649 (tt0) REVERT: A 1441 GLN cc_start: 0.4030 (mp10) cc_final: 0.3710 (mm-40) REVERT: A 1618 PHE cc_start: 0.5778 (OUTLIER) cc_final: 0.5389 (m-80) outliers start: 54 outliers final: 32 residues processed: 274 average time/residue: 0.0621 time to fit residues: 25.1505 Evaluate side-chains 253 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 934 LEU Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1243 TYR Chi-restraints excluded: chain A residue 1298 MET Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1438 GLU Chi-restraints excluded: chain A residue 1609 VAL Chi-restraints excluded: chain A residue 1618 PHE Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1667 PHE Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain B residue 48 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1465 ASN A1474 ASN A1478 GLN A1724 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.187494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.137468 restraints weight = 14493.325| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.43 r_work: 0.3673 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9979 Z= 0.146 Angle : 0.644 9.467 13503 Z= 0.323 Chirality : 0.041 0.215 1562 Planarity : 0.004 0.058 1630 Dihedral : 12.503 136.589 1453 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 5.52 % Allowed : 25.80 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.17 % 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: -0.71 (0.25), residues: 1181 helix: 0.44 (0.18), residues: 804 sheet: -3.47 (0.95), residues: 26 loop : -2.32 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1631 TYR 0.029 0.002 TYR A 777 PHE 0.020 0.001 PHE A1455 TRP 0.013 0.001 TRP A1260 HIS 0.003 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 9961) covalent geometry : angle 0.62861 / 0.32 (13461) SS BOND : bond 0.00447 / 0.29 ( 9) SS BOND : angle 1.66096 / 0.90 ( 18) hydrogen bonds : bond 0.03934 / 2.62 ( 622) hydrogen bonds : angle 5.03638 / 3.61 ( 1767) Misc. bond : bond 0.00040 / 0.02 ( 1) link_BETA1-4 : bond 0.00730 / 0.37 ( 4) link_BETA1-4 : angle 2.80481 / 1.61 ( 12) link_NAG-ASN : bond 0.00711 / 0.35 ( 4) link_NAG-ASN : angle 3.36316 / 2.01 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 237 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8565 (mmmt) cc_final: 0.7876 (ttpt) REVERT: A 199 PHE cc_start: 0.8269 (t80) cc_final: 0.8006 (t80) REVERT: A 223 ARG cc_start: 0.7338 (mmm-85) cc_final: 0.6956 (ttm-80) REVERT: A 341 ARG cc_start: 0.8334 (ptm160) cc_final: 0.7106 (mmt-90) REVERT: A 705 MET cc_start: 0.5247 (mmp) cc_final: 0.4306 (tpp) REVERT: A 716 MET cc_start: 0.3845 (ptt) cc_final: 0.3224 (ppp) REVERT: A 795 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7280 (tmm) REVERT: A 817 PHE cc_start: 0.8049 (m-80) cc_final: 0.7775 (m-80) REVERT: A 1193 TRP cc_start: 0.7202 (t-100) cc_final: 0.6888 (t-100) REVERT: A 1234 ARG cc_start: 0.7206 (ptp-170) cc_final: 0.6719 (ptp-170) REVERT: A 1241 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7914 (mm) REVERT: A 1298 MET cc_start: 0.2564 (OUTLIER) cc_final: 0.0808 (ptm) REVERT: A 1337 MET cc_start: 0.7919 (mmm) cc_final: 0.7371 (mmm) REVERT: A 1396 TYR cc_start: 0.8225 (m-80) cc_final: 0.7976 (m-80) REVERT: A 1438 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.4437 (tt0) REVERT: A 1441 GLN cc_start: 0.4119 (mp10) cc_final: 0.3779 (mm-40) REVERT: A 1618 PHE cc_start: 0.5762 (OUTLIER) cc_final: 0.5363 (m-80) REVERT: A 1724 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7568 (p0) REVERT: B 15 HIS cc_start: 0.5844 (m90) cc_final: 0.5311 (p-80) outliers start: 55 outliers final: 30 residues processed: 274 average time/residue: 0.0683 time to fit residues: 27.9935 Evaluate side-chains 260 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 224 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1243 TYR Chi-restraints excluded: chain A residue 1298 MET Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1438 GLU Chi-restraints excluded: chain A residue 1609 VAL Chi-restraints excluded: chain A residue 1618 PHE Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1667 PHE Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1724 ASN Chi-restraints excluded: chain B residue 48 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 83 optimal weight: 10.0000 chunk 41 optimal weight: 0.0570 chunk 11 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 40 optimal weight: 0.4980 chunk 58 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1381 ASN ** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1465 ASN A1724 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.189089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.139239 restraints weight = 14666.457| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.47 r_work: 0.3661 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 9979 Z= 0.132 Angle : 0.649 11.749 13503 Z= 0.321 Chirality : 0.041 0.218 1562 Planarity : 0.004 0.054 1630 Dihedral : 11.806 127.097 1453 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 5.92 % Allowed : 26.41 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.25), residues: 1181 helix: 0.67 (0.18), residues: 808 sheet: -3.49 (0.96), residues: 26 loop : -2.21 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 226 TYR 0.027 0.001 TYR A 777 PHE 0.028 0.001 PHE A1455 TRP 0.013 0.001 TRP A1260 HIS 0.003 0.001 HIS B 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 9961) covalent geometry : angle 0.63321 / 0.32 (13461) SS BOND : bond 0.00385 / 0.26 ( 9) SS BOND : angle 2.28277 / 1.22 ( 18) hydrogen bonds : bond 0.03794 / 2.54 ( 622) hydrogen bonds : angle 4.93362 / 3.54 ( 1767) Misc. bond : bond 0.00033 / 0.02 ( 1) link_BETA1-4 : bond 0.00549 / 0.27 ( 4) link_BETA1-4 : angle 2.68386 / 1.54 ( 12) link_NAG-ASN : bond 0.00803 / 0.39 ( 4) link_NAG-ASN : angle 3.11679 / 1.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 241 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8547 (mmmt) cc_final: 0.7773 (ttpt) REVERT: A 199 PHE cc_start: 0.8280 (t80) cc_final: 0.8025 (t80) REVERT: A 341 ARG cc_start: 0.8454 (ptm160) cc_final: 0.6977 (mpt180) REVERT: A 383 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8555 (mt) REVERT: A 705 MET cc_start: 0.5312 (mmp) cc_final: 0.4431 (tpp) REVERT: A 795 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7310 (tmm) REVERT: A 817 PHE cc_start: 0.8078 (m-80) cc_final: 0.7848 (m-80) REVERT: A 1193 TRP cc_start: 0.7245 (t-100) cc_final: 0.6936 (t-100) REVERT: A 1234 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6729 (ptp-170) REVERT: A 1241 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7918 (mm) REVERT: A 1298 MET cc_start: 0.2628 (OUTLIER) cc_final: 0.0939 (ptm) REVERT: A 1337 MET cc_start: 0.7941 (mmm) cc_final: 0.7387 (mmm) REVERT: A 1438 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.4583 (tt0) REVERT: A 1441 GLN cc_start: 0.4014 (mp10) cc_final: 0.3679 (mm-40) REVERT: A 1618 PHE cc_start: 0.5721 (OUTLIER) cc_final: 0.5357 (m-80) REVERT: A 1649 LEU cc_start: 0.8006 (mt) cc_final: 0.7555 (mt) REVERT: B 15 HIS cc_start: 0.5705 (m90) cc_final: 0.5263 (p90) REVERT: B 39 PHE cc_start: 0.6324 (OUTLIER) cc_final: 0.5928 (m-80) outliers start: 59 outliers final: 38 residues processed: 279 average time/residue: 0.0662 time to fit residues: 27.5932 Evaluate side-chains 273 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 227 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 789 ILE Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 1234 ARG Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1243 TYR Chi-restraints excluded: chain A residue 1298 MET Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1438 GLU Chi-restraints excluded: chain A residue 1609 VAL Chi-restraints excluded: chain A residue 1618 PHE Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1667 PHE Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1746 SER Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 48 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 2.9990 chunk 109 optimal weight: 0.0060 chunk 39 optimal weight: 8.9990 chunk 90 optimal weight: 0.0170 chunk 30 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 overall best weight: 0.9438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1465 ASN A1474 ASN A1478 GLN A1724 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.189038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.138825 restraints weight = 14734.602| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.47 r_work: 0.3696 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9979 Z= 0.138 Angle : 0.652 10.145 13503 Z= 0.324 Chirality : 0.041 0.209 1562 Planarity : 0.004 0.052 1630 Dihedral : 11.274 119.947 1453 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 6.02 % Allowed : 27.41 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.25), residues: 1181 helix: 0.78 (0.18), residues: 806 sheet: -3.43 (0.97), residues: 26 loop : -2.12 (0.36), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1631 TYR 0.026 0.001 TYR A 777 PHE 0.022 0.001 PHE A1455 TRP 0.014 0.001 TRP A1260 HIS 0.003 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 9961) covalent geometry : angle 0.63863 / 0.32 (13461) SS BOND : bond 0.00415 / 0.25 ( 9) SS BOND : angle 1.84937 / 0.98 ( 18) hydrogen bonds : bond 0.03785 / 2.52 ( 622) hydrogen bonds : angle 4.92908 / 3.53 ( 1767) Misc. bond : bond 0.00039 / 0.02 ( 1) link_BETA1-4 : bond 0.00780 / 0.39 ( 4) link_BETA1-4 : angle 2.71604 / 1.57 ( 12) link_NAG-ASN : bond 0.00667 / 0.33 ( 4) link_NAG-ASN : angle 2.97379 / 1.78 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 234 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8578 (mmmt) cc_final: 0.7755 (ttpt) REVERT: A 199 PHE cc_start: 0.8201 (t80) cc_final: 0.7935 (t80) REVERT: A 383 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8570 (mt) REVERT: A 705 MET cc_start: 0.5283 (mmp) cc_final: 0.4412 (tpp) REVERT: A 716 MET cc_start: 0.4172 (ptt) cc_final: 0.3598 (ppp) REVERT: A 795 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7275 (tmm) REVERT: A 817 PHE cc_start: 0.8088 (m-80) cc_final: 0.7875 (m-80) REVERT: A 1193 TRP cc_start: 0.7149 (t-100) cc_final: 0.6869 (t-100) REVERT: A 1234 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6832 (ptp-170) REVERT: A 1241 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8016 (mm) REVERT: A 1298 MET cc_start: 0.2646 (OUTLIER) cc_final: 0.0829 (ptm) REVERT: A 1337 MET cc_start: 0.7957 (mmm) cc_final: 0.7409 (mmm) REVERT: A 1593 TRP cc_start: 0.6781 (m100) cc_final: 0.5924 (m-10) REVERT: A 1618 PHE cc_start: 0.5681 (OUTLIER) cc_final: 0.5331 (m-80) REVERT: A 1634 ARG cc_start: 0.7947 (ttm-80) cc_final: 0.7641 (ttm-80) REVERT: A 1649 LEU cc_start: 0.8023 (mt) cc_final: 0.7565 (mt) REVERT: B 15 HIS cc_start: 0.5635 (m90) cc_final: 0.5218 (p90) REVERT: B 39 PHE cc_start: 0.6325 (OUTLIER) cc_final: 0.5951 (m-80) outliers start: 60 outliers final: 42 residues processed: 269 average time/residue: 0.0625 time to fit residues: 25.5959 Evaluate side-chains 269 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 220 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1234 ARG Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1243 TYR Chi-restraints excluded: chain A residue 1298 MET Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1438 GLU Chi-restraints excluded: chain A residue 1609 VAL Chi-restraints excluded: chain A residue 1618 PHE Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1667 PHE Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1746 SER Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 48 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 43 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 109 optimal weight: 0.0010 chunk 87 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1465 ASN A1474 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.189343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.139380 restraints weight = 14663.362| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.46 r_work: 0.3682 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9979 Z= 0.140 Angle : 0.673 11.018 13503 Z= 0.330 Chirality : 0.042 0.207 1562 Planarity : 0.004 0.053 1630 Dihedral : 10.983 115.320 1453 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 5.82 % Allowed : 27.51 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.17 % 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: -0.16 (0.25), residues: 1181 helix: 0.83 (0.18), residues: 805 sheet: -3.17 (0.99), residues: 26 loop : -2.04 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1631 TYR 0.025 0.001 TYR A 777 PHE 0.022 0.001 PHE A1455 TRP 0.017 0.001 TRP A1260 HIS 0.003 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 9961) covalent geometry : angle 0.66110 / 0.33 (13461) SS BOND : bond 0.00325 / 0.21 ( 9) SS BOND : angle 1.75933 / 0.91 ( 18) hydrogen bonds : bond 0.03776 / 2.52 ( 622) hydrogen bonds : angle 4.90657 / 3.50 ( 1767) Misc. bond : bond 0.00037 / 0.02 ( 1) link_BETA1-4 : bond 0.00692 / 0.35 ( 4) link_BETA1-4 : angle 2.68467 / 1.55 ( 12) link_NAG-ASN : bond 0.00662 / 0.32 ( 4) link_NAG-ASN : angle 2.81323 / 1.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 232 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8541 (mmmt) cc_final: 0.7745 (ttpt) REVERT: A 199 PHE cc_start: 0.8176 (t80) cc_final: 0.7928 (t80) REVERT: A 383 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8565 (mt) REVERT: A 705 MET cc_start: 0.5233 (mmp) cc_final: 0.4407 (tpp) REVERT: A 795 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7218 (tmm) REVERT: A 817 PHE cc_start: 0.8085 (m-80) cc_final: 0.7864 (m-80) REVERT: A 1234 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6847 (ptp-170) REVERT: A 1241 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8010 (mm) REVERT: A 1298 MET cc_start: 0.2491 (OUTLIER) cc_final: 0.0754 (ptm) REVERT: A 1337 MET cc_start: 0.8044 (mmm) cc_final: 0.7499 (mmm) REVERT: A 1593 TRP cc_start: 0.6770 (m100) cc_final: 0.6027 (m-10) REVERT: A 1618 PHE cc_start: 0.5603 (OUTLIER) cc_final: 0.5251 (m-80) REVERT: A 1649 LEU cc_start: 0.8001 (mt) cc_final: 0.7548 (mt) outliers start: 58 outliers final: 44 residues processed: 270 average time/residue: 0.0663 time to fit residues: 26.9775 Evaluate side-chains 272 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 796 GLU Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1234 ARG Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1243 TYR Chi-restraints excluded: chain A residue 1298 MET Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1438 GLU Chi-restraints excluded: chain A residue 1474 ASN Chi-restraints excluded: chain A residue 1609 VAL Chi-restraints excluded: chain A residue 1618 PHE Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1667 PHE Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1746 SER Chi-restraints excluded: chain B residue 48 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 0.0050 chunk 92 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 64 optimal weight: 0.0060 chunk 101 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 overall best weight: 0.4210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1465 ASN A1474 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.191277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.141490 restraints weight = 14735.288| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.47 r_work: 0.3720 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 9979 Z= 0.129 Angle : 0.685 14.428 13503 Z= 0.335 Chirality : 0.042 0.209 1562 Planarity : 0.004 0.051 1630 Dihedral : 10.630 107.702 1453 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.22 % Allowed : 29.22 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.17 % 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: -0.04 (0.25), residues: 1181 helix: 0.92 (0.18), residues: 805 sheet: -3.10 (0.97), residues: 26 loop : -2.00 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1631 TYR 0.024 0.001 TYR A 777 PHE 0.025 0.001 PHE A1455 TRP 0.020 0.001 TRP A1260 HIS 0.002 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 9961) covalent geometry : angle 0.67140 / 0.33 (13461) SS BOND : bond 0.00261 / 0.17 ( 9) SS BOND : angle 2.34805 / 1.21 ( 18) hydrogen bonds : bond 0.03740 / 2.50 ( 622) hydrogen bonds : angle 4.86354 / 3.48 ( 1767) Misc. bond : bond 0.00032 / 0.02 ( 1) link_BETA1-4 : bond 0.00722 / 0.36 ( 4) link_BETA1-4 : angle 2.61297 / 1.52 ( 12) link_NAG-ASN : bond 0.00676 / 0.33 ( 4) link_NAG-ASN : angle 2.65884 / 1.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 245 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8483 (mmmt) cc_final: 0.7747 (ttpt) REVERT: A 199 PHE cc_start: 0.8233 (t80) cc_final: 0.8022 (t80) REVERT: A 251 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7566 (tt) REVERT: A 383 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8489 (mt) REVERT: A 705 MET cc_start: 0.5287 (mmp) cc_final: 0.4504 (tpp) REVERT: A 716 MET cc_start: 0.3628 (ptt) cc_final: 0.2958 (ppp) REVERT: A 795 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7079 (tmm) REVERT: A 817 PHE cc_start: 0.8000 (m-80) cc_final: 0.7773 (m-80) REVERT: A 1234 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6841 (ptp-170) REVERT: A 1241 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8001 (mm) REVERT: A 1245 ASP cc_start: 0.8409 (t0) cc_final: 0.8192 (t0) REVERT: A 1248 PHE cc_start: 0.8434 (m-10) cc_final: 0.7961 (m-80) REVERT: A 1273 TRP cc_start: 0.7441 (m-90) cc_final: 0.7147 (m-90) REVERT: A 1298 MET cc_start: 0.2548 (OUTLIER) cc_final: 0.0975 (ptm) REVERT: A 1337 MET cc_start: 0.7953 (mmm) cc_final: 0.7437 (mmm) REVERT: A 1552 ASP cc_start: 0.5966 (p0) cc_final: 0.5765 (p0) REVERT: A 1593 TRP cc_start: 0.6746 (m100) cc_final: 0.6018 (m-10) REVERT: A 1618 PHE cc_start: 0.5615 (OUTLIER) cc_final: 0.5256 (m-80) REVERT: A 1634 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7725 (ttm-80) REVERT: A 1649 LEU cc_start: 0.8062 (mt) cc_final: 0.7616 (mt) outliers start: 52 outliers final: 38 residues processed: 275 average time/residue: 0.0714 time to fit residues: 29.2342 Evaluate side-chains 272 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 227 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1234 ARG Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1243 TYR Chi-restraints excluded: chain A residue 1298 MET Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1438 GLU Chi-restraints excluded: chain A residue 1618 PHE Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1667 PHE Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1746 SER Chi-restraints excluded: chain B residue 48 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 36 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 117 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1441 GLN A1465 ASN A1474 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.188256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.138097 restraints weight = 14536.764| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.43 r_work: 0.3654 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9979 Z= 0.161 Angle : 0.691 10.598 13503 Z= 0.342 Chirality : 0.043 0.191 1562 Planarity : 0.004 0.054 1630 Dihedral : 10.643 107.468 1453 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 5.52 % Allowed : 29.62 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.17 % 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: -0.12 (0.25), residues: 1181 helix: 0.83 (0.18), residues: 803 sheet: -3.28 (0.97), residues: 26 loop : -1.91 (0.37), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1631 TYR 0.024 0.002 TYR A 777 PHE 0.031 0.002 PHE A1753 TRP 0.027 0.001 TRP A1260 HIS 0.003 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 9961) covalent geometry : angle 0.67866 / 0.34 (13461) SS BOND : bond 0.00281 / 0.18 ( 9) SS BOND : angle 2.04655 / 1.09 ( 18) hydrogen bonds : bond 0.03836 / 2.55 ( 622) hydrogen bonds : angle 4.93682 / 3.54 ( 1767) Misc. bond : bond 0.00047 / 0.02 ( 1) link_BETA1-4 : bond 0.00709 / 0.36 ( 4) link_BETA1-4 : angle 2.67049 / 1.54 ( 12) link_NAG-ASN : bond 0.00598 / 0.29 ( 4) link_NAG-ASN : angle 2.64083 / 1.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 225 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8525 (mmmt) cc_final: 0.7716 (ttpt) REVERT: A 199 PHE cc_start: 0.8296 (t80) cc_final: 0.8065 (t80) REVERT: A 251 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7531 (tt) REVERT: A 383 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8602 (mt) REVERT: A 705 MET cc_start: 0.5242 (mmp) cc_final: 0.4536 (tpp) REVERT: A 795 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7234 (tmm) REVERT: A 1234 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6936 (ptp-170) REVERT: A 1241 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8024 (mm) REVERT: A 1245 ASP cc_start: 0.8408 (t0) cc_final: 0.8148 (t0) REVERT: A 1248 PHE cc_start: 0.8547 (m-10) cc_final: 0.7961 (m-80) REVERT: A 1273 TRP cc_start: 0.7397 (m-90) cc_final: 0.7093 (m-90) REVERT: A 1298 MET cc_start: 0.2788 (OUTLIER) cc_final: 0.1074 (ptm) REVERT: A 1337 MET cc_start: 0.7895 (mmm) cc_final: 0.7390 (mmm) REVERT: A 1441 GLN cc_start: 0.5609 (mm110) cc_final: 0.3828 (mp10) REVERT: A 1593 TRP cc_start: 0.6757 (m100) cc_final: 0.6031 (m-10) REVERT: A 1618 PHE cc_start: 0.5617 (OUTLIER) cc_final: 0.5285 (m-80) REVERT: A 1649 LEU cc_start: 0.8043 (mt) cc_final: 0.7608 (mt) REVERT: B 15 HIS cc_start: 0.5783 (m90) cc_final: 0.5241 (p-80) outliers start: 55 outliers final: 39 residues processed: 255 average time/residue: 0.0785 time to fit residues: 29.8862 Evaluate side-chains 269 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 223 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1234 ARG Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1243 TYR Chi-restraints excluded: chain A residue 1298 MET Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1438 GLU Chi-restraints excluded: chain A residue 1609 VAL Chi-restraints excluded: chain A residue 1618 PHE Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1667 PHE Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1746 SER Chi-restraints excluded: chain B residue 48 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1376 ASN A1439 GLN A1465 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.189311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.139142 restraints weight = 14578.159| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.44 r_work: 0.3704 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9979 Z= 0.140 Angle : 0.685 12.147 13503 Z= 0.336 Chirality : 0.043 0.208 1562 Planarity : 0.004 0.053 1630 Dihedral : 10.462 103.831 1453 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.72 % Allowed : 30.92 % Favored : 64.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.17 % 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: -0.07 (0.25), residues: 1181 helix: 0.84 (0.18), residues: 807 sheet: -3.09 (1.01), residues: 26 loop : -1.86 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1631 TYR 0.024 0.002 TYR A 777 PHE 0.028 0.001 PHE A1455 TRP 0.033 0.001 TRP A1260 HIS 0.003 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 9961) covalent geometry : angle 0.67469 / 0.33 (13461) SS BOND : bond 0.00423 / 0.25 ( 9) SS BOND : angle 1.80450 / 1.22 ( 18) hydrogen bonds : bond 0.03825 / 2.55 ( 622) hydrogen bonds : angle 4.90158 / 3.52 ( 1767) Misc. bond : bond 0.00040 / 0.02 ( 1) link_BETA1-4 : bond 0.00721 / 0.36 ( 4) link_BETA1-4 : angle 2.59282 / 1.51 ( 12) link_NAG-ASN : bond 0.00669 / 0.33 ( 4) link_NAG-ASN : angle 2.51383 / 1.52 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 230 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8466 (mmmt) cc_final: 0.7725 (ttpt) REVERT: A 199 PHE cc_start: 0.8199 (t80) cc_final: 0.7991 (t80) REVERT: A 251 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7590 (tt) REVERT: A 383 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8579 (mt) REVERT: A 705 MET cc_start: 0.5213 (mmp) cc_final: 0.4563 (tpp) REVERT: A 716 MET cc_start: 0.3780 (ptt) cc_final: 0.3051 (ppp) REVERT: A 795 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7111 (tmm) REVERT: A 817 PHE cc_start: 0.7950 (m-80) cc_final: 0.7607 (m-80) REVERT: A 1234 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.7054 (ptp-170) REVERT: A 1241 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8009 (mm) REVERT: A 1245 ASP cc_start: 0.8394 (t0) cc_final: 0.8144 (t0) REVERT: A 1248 PHE cc_start: 0.8470 (m-10) cc_final: 0.7878 (m-80) REVERT: A 1273 TRP cc_start: 0.7389 (m-90) cc_final: 0.7095 (m-90) REVERT: A 1298 MET cc_start: 0.2915 (OUTLIER) cc_final: 0.1169 (ptm) REVERT: A 1337 MET cc_start: 0.7834 (mmm) cc_final: 0.7338 (mmm) REVERT: A 1593 TRP cc_start: 0.6751 (m100) cc_final: 0.6043 (m-10) REVERT: A 1618 PHE cc_start: 0.5623 (OUTLIER) cc_final: 0.5262 (m-80) REVERT: A 1649 LEU cc_start: 0.8058 (mt) cc_final: 0.7617 (mt) REVERT: B 15 HIS cc_start: 0.5680 (m90) cc_final: 0.5178 (p-80) outliers start: 47 outliers final: 36 residues processed: 257 average time/residue: 0.0806 time to fit residues: 30.9229 Evaluate side-chains 266 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1234 ARG Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1241 LEU Chi-restraints excluded: chain A residue 1243 TYR Chi-restraints excluded: chain A residue 1298 MET Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1326 VAL Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1438 GLU Chi-restraints excluded: chain A residue 1618 PHE Chi-restraints excluded: chain A residue 1645 ILE Chi-restraints excluded: chain A residue 1667 PHE Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain A residue 1684 VAL Chi-restraints excluded: chain A residue 1746 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 91 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 101 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1441 GLN A1465 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.189913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.143264 restraints weight = 14670.503| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 3.07 r_work: 0.3667 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9979 Z= 0.140 Angle : 0.698 15.668 13503 Z= 0.341 Chirality : 0.043 0.210 1562 Planarity : 0.004 0.052 1630 Dihedral : 10.301 99.571 1453 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.62 % Allowed : 31.43 % Favored : 63.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.17 % 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: -0.03 (0.25), residues: 1181 helix: 0.86 (0.18), residues: 806 sheet: -2.98 (1.04), residues: 26 loop : -1.83 (0.37), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1631 TYR 0.027 0.002 TYR A 777 PHE 0.027 0.001 PHE A1455 TRP 0.039 0.001 TRP A1260 HIS 0.003 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 9961) covalent geometry : angle 0.68805 / 0.34 (13461) SS BOND : bond 0.00435 / 0.23 ( 9) SS BOND : angle 1.50882 / 0.98 ( 18) hydrogen bonds : bond 0.03803 / 2.54 ( 622) hydrogen bonds : angle 4.87291 / 3.49 ( 1767) Misc. bond : bond 0.00041 / 0.02 ( 1) link_BETA1-4 : bond 0.00715 / 0.36 ( 4) link_BETA1-4 : angle 2.58168 / 1.50 ( 12) link_NAG-ASN : bond 0.00658 / 0.32 ( 4) link_NAG-ASN : angle 2.56145 / 1.54 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3370.18 seconds wall clock time: 58 minutes 0.62 seconds (3480.62 seconds total)