Starting phenix.real_space_refine on Wed Mar 4 02:23:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k18_22621/03_2026/7k18_22621.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k18_22621/03_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_22621/03_2026/7k18_22621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k18_22621/03_2026/7k18_22621.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k18_22621/03_2026/7k18_22621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k18_22621/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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: 255 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: 2.18, per 1000 atoms: 0.22 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: 0.82 Conformation dependent library (CDL) restraints added in 383.9 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: 0.31 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: 1.52 Time building geometry restraints manager: 1.09 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 - 34.37: 5670 34.37 - 68.75: 284 68.75 - 103.12: 28 103.12 - 137.50: 11 137.50 - 171.87: 6 Dihedral angle restraints: 5999 sinusoidal: 2534 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 5996 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: 1.190 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.520 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 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 : 20.820 171.870 3736 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 covalent geometry : bond 0.00646 ( 9961) covalent geometry : angle 1.09438 (13461) SS BOND : bond 0.42408 ( 9) SS BOND : angle 18.24794 ( 18) hydrogen bonds : bond 0.10761 ( 622) hydrogen bonds : angle 6.29344 ( 1767) Misc. bond : bond 0.00305 ( 1) link_BETA1-4 : bond 0.00760 ( 4) link_BETA1-4 : angle 4.46076 ( 12) link_NAG-ASN : bond 0.14302 ( 4) link_NAG-ASN : angle 12.14944 ( 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 : 0.337 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: 0.0912 time to fit residues: 40.8699 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 : 0.324 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4441 r_free = 0.4441 target = 0.187094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.137127 restraints weight = 14605.796| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.44 r_work: 0.3640 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 9979 Z= 0.158 Angle : 0.707 9.500 13503 Z= 0.358 Chirality : 0.043 0.231 1562 Planarity : 0.005 0.068 1630 Dihedral : 19.290 179.138 1725 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.82 % Allowed : 24.20 % Favored : 70.98 % 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: -1.67 (0.23), residues: 1181 helix: -0.41 (0.17), residues: 807 sheet: None (None), residues: 0 loop : -2.54 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1625 TYR 0.030 0.002 TYR A 379 PHE 0.019 0.002 PHE A1596 TRP 0.014 0.001 TRP A1715 HIS 0.003 0.001 HIS B 15 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9961) covalent geometry : angle 0.67993 (13461) SS BOND : bond 0.00654 ( 9) SS BOND : angle 3.00436 ( 18) hydrogen bonds : bond 0.04328 ( 622) hydrogen bonds : angle 5.28709 ( 1767) Misc. bond : bond 0.00009 ( 1) link_BETA1-4 : bond 0.00773 ( 4) link_BETA1-4 : angle 3.50536 ( 12) link_NAG-ASN : bond 0.00459 ( 4) link_NAG-ASN : angle 4.26065 ( 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 303 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 255 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8576 (mmmt) cc_final: 0.7873 (ttpt) REVERT: A 177 ILE cc_start: 0.8249 (mt) cc_final: 0.7694 (tp) REVERT: A 199 PHE cc_start: 0.8305 (t80) cc_final: 0.8095 (t80) REVERT: A 206 TYR cc_start: 0.7992 (m-80) cc_final: 0.7791 (m-10) REVERT: A 219 LEU cc_start: 0.7634 (pt) cc_final: 0.6977 (tp) REVERT: A 223 ARG cc_start: 0.7440 (mmm-85) cc_final: 0.6768 (ttm-80) REVERT: A 226 ARG cc_start: 0.7850 (mtt180) cc_final: 0.7560 (mtt-85) REVERT: A 341 ARG cc_start: 0.8491 (ptm160) cc_final: 0.7260 (mmm-85) REVERT: A 705 MET cc_start: 0.5318 (mmp) cc_final: 0.4250 (tpp) REVERT: A 817 PHE cc_start: 0.7888 (m-80) cc_final: 0.7570 (m-80) REVERT: A 1193 TRP cc_start: 0.7287 (t-100) cc_final: 0.6903 (t-100) REVERT: A 1197 ARG cc_start: 0.6668 (ttp80) cc_final: 0.6453 (mtp-110) REVERT: A 1234 ARG cc_start: 0.7053 (ptp-170) cc_final: 0.6834 (ptp-170) REVERT: A 1241 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7982 (mm) REVERT: A 1298 MET cc_start: 0.2792 (ttm) cc_final: 0.0944 (ptm) REVERT: A 1337 MET cc_start: 0.7822 (mmm) cc_final: 0.7263 (mmm) REVERT: A 1438 GLU cc_start: 0.6138 (pt0) cc_final: 0.5549 (tt0) REVERT: A 1441 GLN cc_start: 0.4107 (mp10) cc_final: 0.3645 (mp10) REVERT: A 1493 GLN cc_start: 0.6819 (mm-40) cc_final: 0.6364 (mp10) REVERT: A 1618 PHE cc_start: 0.5735 (OUTLIER) cc_final: 0.5377 (m-80) outliers start: 48 outliers final: 25 residues processed: 289 average time/residue: 0.0834 time to fit residues: 34.9758 Evaluate side-chains 251 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.4980 chunk 83 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A 751 GLN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1465 ASN A1474 ASN A1478 GLN A1543 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.186792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.137610 restraints weight = 14504.074| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.41 r_work: 0.3668 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9979 Z= 0.157 Angle : 0.674 9.652 13503 Z= 0.338 Chirality : 0.042 0.212 1562 Planarity : 0.004 0.060 1630 Dihedral : 17.511 178.669 1704 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 5.42 % Allowed : 25.80 % Favored : 68.78 % 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: -1.00 (0.24), residues: 1181 helix: 0.17 (0.17), residues: 806 sheet: -3.68 (1.36), residues: 14 loop : -2.35 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1631 TYR 0.028 0.002 TYR A 777 PHE 0.027 0.002 PHE A1753 TRP 0.015 0.001 TRP A1260 HIS 0.003 0.001 HIS A 889 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9961) covalent geometry : angle 0.65164 (13461) SS BOND : bond 0.00451 ( 9) SS BOND : angle 2.02939 ( 18) hydrogen bonds : bond 0.04051 ( 622) hydrogen bonds : angle 5.10755 ( 1767) Misc. bond : bond 0.00062 ( 1) link_BETA1-4 : bond 0.00818 ( 4) link_BETA1-4 : angle 3.66281 ( 12) link_NAG-ASN : bond 0.00695 ( 4) link_NAG-ASN : angle 3.83771 ( 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 294 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 240 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8565 (mmmt) cc_final: 0.7891 (ttpt) REVERT: A 199 PHE cc_start: 0.8283 (t80) cc_final: 0.8018 (t80) REVERT: A 223 ARG cc_start: 0.7342 (mmm-85) cc_final: 0.6929 (ttm-80) REVERT: A 226 ARG cc_start: 0.7950 (mtt180) cc_final: 0.7737 (mtt-85) REVERT: A 341 ARG cc_start: 0.8381 (ptm160) cc_final: 0.7179 (mpt180) REVERT: A 705 MET cc_start: 0.5385 (mmp) cc_final: 0.4374 (tpp) REVERT: A 795 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7293 (tmm) REVERT: A 817 PHE cc_start: 0.8092 (m-80) cc_final: 0.7771 (m-80) REVERT: A 1193 TRP cc_start: 0.7265 (t-100) cc_final: 0.6958 (t-100) REVERT: A 1234 ARG cc_start: 0.7176 (ptp-170) cc_final: 0.6797 (ptp-170) REVERT: A 1241 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7913 (mm) REVERT: A 1298 MET cc_start: 0.2736 (OUTLIER) cc_final: 0.0895 (ptm) REVERT: A 1337 MET cc_start: 0.7952 (mmm) cc_final: 0.7409 (mmm) REVERT: A 1396 TYR cc_start: 0.8269 (m-80) cc_final: 0.8067 (m-80) REVERT: A 1434 ARG cc_start: 0.6557 (mmm160) cc_final: 0.5884 (mmm-85) REVERT: A 1438 GLU cc_start: 0.5962 (OUTLIER) cc_final: 0.4402 (tt0) REVERT: A 1441 GLN cc_start: 0.4087 (mp10) cc_final: 0.3796 (mm-40) REVERT: A 1618 PHE cc_start: 0.5778 (OUTLIER) cc_final: 0.5389 (m-80) outliers start: 54 outliers final: 31 residues processed: 275 average time/residue: 0.0821 time to fit residues: 32.8725 Evaluate side-chains 256 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 751 GLN Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 796 GLU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 46 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.185556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.135117 restraints weight = 14489.653| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.41 r_work: 0.3654 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9979 Z= 0.179 Angle : 0.684 10.438 13503 Z= 0.340 Chirality : 0.043 0.220 1562 Planarity : 0.004 0.061 1630 Dihedral : 16.689 178.220 1695 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 6.22 % Allowed : 25.20 % Favored : 68.57 % 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: -0.85 (0.24), residues: 1181 helix: 0.33 (0.18), residues: 807 sheet: -3.44 (0.96), residues: 26 loop : -2.38 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1631 TYR 0.030 0.002 TYR A 777 PHE 0.019 0.002 PHE A 811 TRP 0.015 0.002 TRP A1260 HIS 0.004 0.001 HIS A 889 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 9961) covalent geometry : angle 0.66458 (13461) SS BOND : bond 0.00411 ( 9) SS BOND : angle 1.85803 ( 18) hydrogen bonds : bond 0.04061 ( 622) hydrogen bonds : angle 5.11337 ( 1767) Misc. bond : bond 0.00074 ( 1) link_BETA1-4 : bond 0.00844 ( 4) link_BETA1-4 : angle 3.62901 ( 12) link_NAG-ASN : bond 0.00696 ( 4) link_NAG-ASN : angle 3.65409 ( 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 296 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 234 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8556 (mmmt) cc_final: 0.7854 (ttpt) REVERT: A 199 PHE cc_start: 0.8257 (t80) cc_final: 0.7982 (t80) REVERT: A 309 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7113 (tp) REVERT: A 341 ARG cc_start: 0.8348 (ptm160) cc_final: 0.7060 (mmt-90) REVERT: A 705 MET cc_start: 0.5312 (mmp) cc_final: 0.4312 (tpp) REVERT: A 716 MET cc_start: 0.3820 (ptt) cc_final: 0.3157 (ppp) REVERT: A 795 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7291 (tmm) REVERT: A 817 PHE cc_start: 0.8139 (m-80) cc_final: 0.7847 (m-80) REVERT: A 1193 TRP cc_start: 0.7206 (t-100) cc_final: 0.6888 (t-100) REVERT: A 1234 ARG cc_start: 0.7202 (ptp-170) cc_final: 0.6696 (ptp-170) REVERT: A 1241 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7958 (mm) REVERT: A 1298 MET cc_start: 0.2643 (OUTLIER) cc_final: 0.0857 (ptm) REVERT: A 1396 TYR cc_start: 0.8309 (m-80) cc_final: 0.8062 (m-80) REVERT: A 1434 ARG cc_start: 0.6388 (mmm160) cc_final: 0.5700 (mmm-85) REVERT: A 1438 GLU cc_start: 0.5974 (OUTLIER) cc_final: 0.4118 (tt0) REVERT: A 1441 GLN cc_start: 0.4148 (mp10) cc_final: 0.3858 (mm-40) REVERT: A 1618 PHE cc_start: 0.5779 (OUTLIER) cc_final: 0.5377 (m-80) REVERT: B 15 HIS cc_start: 0.5877 (m90) cc_final: 0.5326 (p-80) outliers start: 62 outliers final: 35 residues processed: 277 average time/residue: 0.0805 time to fit residues: 32.8377 Evaluate side-chains 259 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 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 309 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 796 GLU 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 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 1554 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 83 optimal weight: 0.0060 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 A1724 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.188338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.139171 restraints weight = 14540.252| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.41 r_work: 0.3686 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 9979 Z= 0.136 Angle : 0.676 12.523 13503 Z= 0.332 Chirality : 0.042 0.238 1562 Planarity : 0.004 0.056 1630 Dihedral : 15.616 178.396 1695 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 5.42 % Allowed : 27.61 % Favored : 66.97 % 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: -0.51 (0.25), residues: 1181 helix: 0.60 (0.18), residues: 806 sheet: -3.56 (0.97), residues: 26 loop : -2.26 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 223 TYR 0.027 0.002 TYR A 777 PHE 0.022 0.001 PHE A1455 TRP 0.017 0.001 TRP A1260 HIS 0.003 0.001 HIS B 15 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9961) covalent geometry : angle 0.65393 (13461) SS BOND : bond 0.00350 ( 9) SS BOND : angle 2.60347 ( 18) hydrogen bonds : bond 0.03869 ( 622) hydrogen bonds : angle 4.96659 ( 1767) Misc. bond : bond 0.00054 ( 1) link_BETA1-4 : bond 0.00896 ( 4) link_BETA1-4 : angle 3.60154 ( 12) link_NAG-ASN : bond 0.00794 ( 4) link_NAG-ASN : angle 3.35925 ( 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 290 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 236 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8541 (mmmt) cc_final: 0.7694 (ttpt) REVERT: A 199 PHE cc_start: 0.8245 (t80) cc_final: 0.7993 (t80) REVERT: A 251 LEU cc_start: 0.7818 (mt) cc_final: 0.7606 (tt) REVERT: A 383 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8565 (mt) REVERT: A 395 MET cc_start: 0.8296 (ttp) cc_final: 0.8084 (ttt) REVERT: A 705 MET cc_start: 0.5299 (mmp) cc_final: 0.4418 (tpp) REVERT: A 795 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7257 (tmm) REVERT: A 817 PHE cc_start: 0.8070 (m-80) cc_final: 0.7867 (m-80) REVERT: A 1193 TRP cc_start: 0.7209 (t-100) cc_final: 0.6903 (t-100) REVERT: A 1234 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6741 (ptp-170) REVERT: A 1241 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7922 (mm) REVERT: A 1298 MET cc_start: 0.2607 (OUTLIER) cc_final: 0.0816 (ptm) REVERT: A 1310 LEU cc_start: 0.8161 (mt) cc_final: 0.7948 (mt) REVERT: A 1396 TYR cc_start: 0.8184 (m-80) cc_final: 0.7928 (m-80) REVERT: A 1438 GLU cc_start: 0.6033 (OUTLIER) cc_final: 0.4554 (tt0) REVERT: A 1618 PHE cc_start: 0.5734 (OUTLIER) cc_final: 0.5353 (m-80) REVERT: A 1649 LEU cc_start: 0.8035 (mt) cc_final: 0.7557 (mt) REVERT: A 1724 ASN cc_start: 0.7672 (OUTLIER) cc_final: 0.7444 (p0) REVERT: B 15 HIS cc_start: 0.5670 (m90) cc_final: 0.5232 (p90) outliers start: 54 outliers final: 30 residues processed: 270 average time/residue: 0.0763 time to fit residues: 30.5865 Evaluate side-chains 261 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 211 VAL 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 383 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 755 LEU 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 904 GLU Chi-restraints excluded: chain A residue 919 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 1.9990 chunk 109 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 90 optimal weight: 0.0000 chunk 30 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 = 0.4463 r_free = 0.4463 target = 0.189458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.140653 restraints weight = 14580.024| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.43 r_work: 0.3680 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9979 Z= 0.133 Angle : 0.669 10.169 13503 Z= 0.326 Chirality : 0.042 0.236 1562 Planarity : 0.004 0.052 1630 Dihedral : 14.973 179.672 1695 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 5.12 % Allowed : 28.41 % Favored : 66.47 % 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: -0.32 (0.25), residues: 1181 helix: 0.74 (0.18), residues: 806 sheet: -3.50 (1.00), residues: 26 loop : -2.17 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1631 TYR 0.026 0.002 TYR A 777 PHE 0.022 0.001 PHE A1455 TRP 0.017 0.001 TRP A1260 HIS 0.002 0.001 HIS B 15 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9961) covalent geometry : angle 0.65022 (13461) SS BOND : bond 0.00375 ( 9) SS BOND : angle 2.09279 ( 18) hydrogen bonds : bond 0.03808 ( 622) hydrogen bonds : angle 4.91885 ( 1767) Misc. bond : bond 0.00057 ( 1) link_BETA1-4 : bond 0.00919 ( 4) link_BETA1-4 : angle 3.56974 ( 12) link_NAG-ASN : bond 0.00735 ( 4) link_NAG-ASN : angle 3.22626 ( 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 287 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 236 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8533 (mmmt) cc_final: 0.7775 (ttpt) REVERT: A 199 PHE cc_start: 0.8277 (t80) cc_final: 0.8016 (t80) REVERT: A 383 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8580 (mt) REVERT: A 705 MET cc_start: 0.5281 (mmp) cc_final: 0.4404 (tpp) REVERT: A 795 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7292 (tmm) REVERT: A 817 PHE cc_start: 0.8080 (m-80) cc_final: 0.7858 (m-80) REVERT: A 1193 TRP cc_start: 0.7188 (t-100) cc_final: 0.6908 (t-100) REVERT: A 1234 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6811 (ptp-170) REVERT: A 1241 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7935 (mm) REVERT: A 1298 MET cc_start: 0.2484 (OUTLIER) cc_final: 0.0779 (ptm) REVERT: A 1310 LEU cc_start: 0.8128 (mt) cc_final: 0.7904 (mt) REVERT: A 1396 TYR cc_start: 0.8127 (m-80) cc_final: 0.7796 (m-80) REVERT: A 1438 GLU cc_start: 0.5069 (OUTLIER) cc_final: 0.4306 (tt0) REVERT: A 1593 TRP cc_start: 0.6768 (m100) cc_final: 0.5958 (m-10) REVERT: A 1618 PHE cc_start: 0.5674 (OUTLIER) cc_final: 0.5334 (m-80) REVERT: A 1649 LEU cc_start: 0.7995 (mt) cc_final: 0.7541 (mt) REVERT: B 15 HIS cc_start: 0.5655 (m90) cc_final: 0.5239 (p90) outliers start: 51 outliers final: 37 residues processed: 269 average time/residue: 0.0768 time to fit residues: 30.7130 Evaluate side-chains 270 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 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 317 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 755 LEU 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 904 GLU Chi-restraints excluded: chain A residue 919 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 43 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A1474 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.187517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.137196 restraints weight = 14589.448| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.45 r_work: 0.3639 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9979 Z= 0.162 Angle : 0.711 13.407 13503 Z= 0.341 Chirality : 0.043 0.248 1562 Planarity : 0.004 0.055 1630 Dihedral : 14.509 177.814 1695 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 5.32 % Allowed : 28.11 % 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: -0.27 (0.25), residues: 1181 helix: 0.74 (0.18), residues: 808 sheet: -3.46 (1.00), residues: 26 loop : -2.08 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1631 TYR 0.026 0.002 TYR A 777 PHE 0.017 0.001 PHE A1455 TRP 0.017 0.001 TRP A1260 HIS 0.004 0.001 HIS A 889 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 9961) covalent geometry : angle 0.69337 (13461) SS BOND : bond 0.00331 ( 9) SS BOND : angle 1.97143 ( 18) hydrogen bonds : bond 0.03851 ( 622) hydrogen bonds : angle 4.97548 ( 1767) Misc. bond : bond 0.00069 ( 1) link_BETA1-4 : bond 0.00923 ( 4) link_BETA1-4 : angle 3.59491 ( 12) link_NAG-ASN : bond 0.00665 ( 4) link_NAG-ASN : angle 3.33999 ( 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 282 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 229 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8554 (mmmt) cc_final: 0.7730 (ttpt) REVERT: A 199 PHE cc_start: 0.8282 (t80) cc_final: 0.8049 (t80) REVERT: A 705 MET cc_start: 0.5308 (mmp) cc_final: 0.4420 (tpp) REVERT: A 795 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7212 (tmm) REVERT: A 817 PHE cc_start: 0.8126 (m-80) cc_final: 0.7897 (m-80) REVERT: A 1193 TRP cc_start: 0.7203 (t-100) cc_final: 0.6933 (t-100) REVERT: A 1234 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6880 (ptp-170) REVERT: A 1241 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8016 (mm) REVERT: A 1298 MET cc_start: 0.2557 (OUTLIER) cc_final: 0.0784 (ptm) REVERT: A 1310 LEU cc_start: 0.8163 (mt) cc_final: 0.7949 (mt) REVERT: A 1438 GLU cc_start: 0.5066 (OUTLIER) cc_final: 0.3937 (tt0) REVERT: A 1552 ASP cc_start: 0.6245 (p0) cc_final: 0.6001 (p0) REVERT: A 1593 TRP cc_start: 0.6769 (m100) cc_final: 0.5950 (m-10) REVERT: A 1618 PHE cc_start: 0.5574 (OUTLIER) cc_final: 0.5231 (m-80) REVERT: A 1634 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7702 (ttm-80) REVERT: A 1649 LEU cc_start: 0.7999 (mt) cc_final: 0.7536 (mt) REVERT: B 15 HIS cc_start: 0.5668 (m90) cc_final: 0.5247 (p90) outliers start: 53 outliers final: 40 residues processed: 260 average time/residue: 0.0798 time to fit residues: 30.7140 Evaluate side-chains 268 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 317 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 755 LEU 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 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 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 1608 THR 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 71 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 64 optimal weight: 0.3980 chunk 101 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** 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** A1441 GLN A1474 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.190047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.140202 restraints weight = 14580.483| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.47 r_work: 0.3696 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9979 Z= 0.132 Angle : 0.691 12.406 13503 Z= 0.331 Chirality : 0.042 0.229 1562 Planarity : 0.004 0.051 1630 Dihedral : 13.692 176.097 1695 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 5.02 % Allowed : 29.42 % 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: -0.09 (0.25), residues: 1181 helix: 0.89 (0.18), residues: 804 sheet: -3.49 (0.99), residues: 26 loop : -2.00 (0.36), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1631 TYR 0.022 0.001 TYR A 777 PHE 0.022 0.001 PHE A1455 TRP 0.017 0.001 TRP A1260 HIS 0.002 0.001 HIS A 889 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9961) covalent geometry : angle 0.67393 (13461) SS BOND : bond 0.00275 ( 9) SS BOND : angle 1.67650 ( 18) hydrogen bonds : bond 0.03795 ( 622) hydrogen bonds : angle 4.89108 ( 1767) Misc. bond : bond 0.00055 ( 1) link_BETA1-4 : bond 0.00895 ( 4) link_BETA1-4 : angle 3.64452 ( 12) link_NAG-ASN : bond 0.00698 ( 4) link_NAG-ASN : angle 3.09610 ( 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 294 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 244 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8505 (mmmt) cc_final: 0.7730 (ttpt) REVERT: A 199 PHE cc_start: 0.8252 (t80) cc_final: 0.8009 (t80) REVERT: A 223 ARG cc_start: 0.7547 (ttm-80) cc_final: 0.6862 (mtp-110) REVERT: A 383 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8577 (mt) REVERT: A 705 MET cc_start: 0.5107 (mmp) cc_final: 0.4429 (tpp) REVERT: A 795 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7110 (tmm) REVERT: A 817 PHE cc_start: 0.8049 (m-80) cc_final: 0.7827 (m-80) REVERT: A 1193 TRP cc_start: 0.7121 (t-100) cc_final: 0.6859 (t-100) REVERT: A 1234 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6944 (ptp-170) REVERT: A 1241 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8024 (mm) REVERT: A 1245 ASP cc_start: 0.8428 (t0) cc_final: 0.8201 (t0) REVERT: A 1248 PHE cc_start: 0.8441 (m-10) cc_final: 0.7894 (m-80) REVERT: A 1298 MET cc_start: 0.2599 (OUTLIER) cc_final: 0.0934 (ptm) REVERT: A 1310 LEU cc_start: 0.8180 (mt) cc_final: 0.7947 (mt) REVERT: A 1438 GLU cc_start: 0.5048 (OUTLIER) cc_final: 0.4197 (tt0) REVERT: A 1552 ASP cc_start: 0.6094 (p0) cc_final: 0.5856 (p0) REVERT: A 1593 TRP cc_start: 0.6747 (m100) cc_final: 0.6050 (m-10) REVERT: A 1618 PHE cc_start: 0.5574 (OUTLIER) cc_final: 0.5250 (m-80) REVERT: A 1649 LEU cc_start: 0.8058 (mt) cc_final: 0.7599 (mt) REVERT: B 15 HIS cc_start: 0.5617 (m90) cc_final: 0.5219 (p90) outliers start: 50 outliers final: 32 residues processed: 276 average time/residue: 0.0789 time to fit residues: 32.1032 Evaluate side-chains 264 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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 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 755 LEU 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 36 optimal weight: 2.9990 chunk 113 optimal weight: 0.0470 chunk 91 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.1280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.188940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.138849 restraints weight = 14502.757| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.44 r_work: 0.3694 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 9979 Z= 0.153 Angle : 0.739 14.863 13503 Z= 0.352 Chirality : 0.044 0.207 1562 Planarity : 0.004 0.053 1630 Dihedral : 13.419 173.184 1695 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 4.62 % Allowed : 30.82 % Favored : 64.56 % 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: -0.15 (0.25), residues: 1181 helix: 0.81 (0.18), residues: 803 sheet: -3.50 (0.98), residues: 26 loop : -1.91 (0.37), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 226 TYR 0.024 0.002 TYR A 777 PHE 0.039 0.002 PHE A1753 TRP 0.024 0.001 TRP A1260 HIS 0.003 0.001 HIS A 889 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9961) covalent geometry : angle 0.72172 (13461) SS BOND : bond 0.00285 ( 9) SS BOND : angle 2.12252 ( 18) hydrogen bonds : bond 0.03871 ( 622) hydrogen bonds : angle 4.95198 ( 1767) Misc. bond : bond 0.00060 ( 1) link_BETA1-4 : bond 0.00932 ( 4) link_BETA1-4 : angle 3.74106 ( 12) link_NAG-ASN : bond 0.00634 ( 4) link_NAG-ASN : angle 3.03319 ( 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 276 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 230 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8514 (mmmt) cc_final: 0.7704 (ttpt) REVERT: A 199 PHE cc_start: 0.8265 (t80) cc_final: 0.8059 (t80) REVERT: A 327 CYS cc_start: 0.6347 (OUTLIER) cc_final: 0.6108 (p) REVERT: A 383 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8594 (mt) REVERT: A 705 MET cc_start: 0.5098 (mmp) cc_final: 0.4429 (tpp) REVERT: A 795 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7127 (tmm) REVERT: A 1193 TRP cc_start: 0.7085 (t-100) cc_final: 0.6822 (t-100) REVERT: A 1234 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6941 (ptp-170) REVERT: A 1241 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8038 (mm) REVERT: A 1245 ASP cc_start: 0.8387 (t0) cc_final: 0.8132 (t0) REVERT: A 1248 PHE cc_start: 0.8503 (m-10) cc_final: 0.7923 (m-80) REVERT: A 1298 MET cc_start: 0.2789 (OUTLIER) cc_final: 0.1029 (ptm) REVERT: A 1310 LEU cc_start: 0.8134 (mt) cc_final: 0.7912 (mt) REVERT: A 1552 ASP cc_start: 0.6157 (p0) cc_final: 0.5919 (p0) REVERT: A 1593 TRP cc_start: 0.6715 (m100) cc_final: 0.5774 (m-10) REVERT: A 1618 PHE cc_start: 0.5664 (OUTLIER) cc_final: 0.5288 (m-80) REVERT: A 1634 ARG cc_start: 0.7970 (ttm-80) cc_final: 0.7611 (ttm-80) REVERT: A 1649 LEU cc_start: 0.8052 (mt) cc_final: 0.7586 (mt) REVERT: B 15 HIS cc_start: 0.5739 (m90) cc_final: 0.5229 (p-80) outliers start: 46 outliers final: 37 residues processed: 257 average time/residue: 0.0774 time to fit residues: 29.4882 Evaluate side-chains 267 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 223 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 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 755 LEU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 21 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 94 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1441 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.190856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.141265 restraints weight = 14567.223| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.45 r_work: 0.3689 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3458 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= 0.134 Angle : 0.733 14.733 13503 Z= 0.349 Chirality : 0.044 0.255 1562 Planarity : 0.004 0.053 1630 Dihedral : 13.025 171.223 1695 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.12 % Allowed : 31.73 % Favored : 64.16 % 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: 0.01 (0.25), residues: 1181 helix: 0.91 (0.18), residues: 797 sheet: -3.24 (1.03), residues: 26 loop : -1.77 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1631 TYR 0.022 0.002 TYR A 777 PHE 0.025 0.001 PHE A1681 TRP 0.033 0.001 TRP A1260 HIS 0.002 0.001 HIS A 889 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9961) covalent geometry : angle 0.71628 (13461) SS BOND : bond 0.00246 ( 9) SS BOND : angle 2.07889 ( 18) hydrogen bonds : bond 0.03814 ( 622) hydrogen bonds : angle 4.88975 ( 1767) Misc. bond : bond 0.00058 ( 1) link_BETA1-4 : bond 0.00983 ( 4) link_BETA1-4 : angle 3.73345 ( 12) link_NAG-ASN : bond 0.00668 ( 4) link_NAG-ASN : angle 2.79975 ( 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 276 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 235 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8493 (mmmt) cc_final: 0.7695 (ttpt) REVERT: A 383 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8555 (mt) REVERT: A 705 MET cc_start: 0.5199 (mmp) cc_final: 0.4566 (tpp) REVERT: A 716 MET cc_start: 0.3735 (ptt) cc_final: 0.3045 (ppp) REVERT: A 795 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7154 (tmm) REVERT: A 817 PHE cc_start: 0.7924 (m-80) cc_final: 0.7572 (m-80) REVERT: A 1234 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6953 (ptp-170) REVERT: A 1241 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8021 (mm) REVERT: A 1245 ASP cc_start: 0.8425 (t0) cc_final: 0.8151 (t0) REVERT: A 1248 PHE cc_start: 0.8494 (m-10) cc_final: 0.7959 (m-80) REVERT: A 1298 MET cc_start: 0.2920 (OUTLIER) cc_final: 0.1149 (ptm) REVERT: A 1310 LEU cc_start: 0.8157 (mt) cc_final: 0.7938 (mt) REVERT: A 1438 GLU cc_start: 0.4968 (OUTLIER) cc_final: 0.4180 (tt0) REVERT: A 1552 ASP cc_start: 0.6040 (p0) cc_final: 0.5801 (p0) REVERT: A 1593 TRP cc_start: 0.6759 (m100) cc_final: 0.6020 (m-10) REVERT: A 1618 PHE cc_start: 0.5741 (OUTLIER) cc_final: 0.5425 (m-80) REVERT: A 1649 LEU cc_start: 0.8030 (mt) cc_final: 0.7587 (mt) REVERT: A 1660 PHE cc_start: 0.7781 (t80) cc_final: 0.7538 (t80) REVERT: A 1727 PRO cc_start: 0.8715 (Cg_exo) cc_final: 0.8513 (Cg_endo) REVERT: B 15 HIS cc_start: 0.5705 (m90) cc_final: 0.5197 (p-80) outliers start: 41 outliers final: 30 residues processed: 261 average time/residue: 0.0745 time to fit residues: 28.8228 Evaluate side-chains 263 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 230 THR Chi-restraints excluded: chain A residue 247 SER 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 755 LEU Chi-restraints excluded: chain A residue 795 MET 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 91 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.190178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.143984 restraints weight = 14654.343| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 3.20 r_work: 0.3692 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9979 Z= 0.140 Angle : 0.745 15.787 13503 Z= 0.353 Chirality : 0.044 0.214 1562 Planarity : 0.004 0.051 1630 Dihedral : 12.801 167.792 1695 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.02 % Allowed : 32.53 % Favored : 63.45 % 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: 0.01 (0.25), residues: 1181 helix: 0.88 (0.18), residues: 801 sheet: -2.68 (1.06), residues: 24 loop : -1.74 (0.37), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1631 TYR 0.022 0.002 TYR A 777 PHE 0.035 0.002 PHE A1596 TRP 0.037 0.001 TRP A1260 HIS 0.003 0.001 HIS A 889 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9961) covalent geometry : angle 0.72980 (13461) SS BOND : bond 0.00299 ( 9) SS BOND : angle 1.88537 ( 18) hydrogen bonds : bond 0.03793 ( 622) hydrogen bonds : angle 4.94050 ( 1767) Misc. bond : bond 0.00055 ( 1) link_BETA1-4 : bond 0.01106 ( 4) link_BETA1-4 : angle 3.78572 ( 12) link_NAG-ASN : bond 0.00655 ( 4) link_NAG-ASN : angle 2.72336 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3611.05 seconds wall clock time: 62 minutes 1.58 seconds (3721.58 seconds total)