Starting phenix.real_space_refine on Thu Jul 2 22:31:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wel_32451/07_2026/7wel_32451.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wel_32451/07_2026/7wel_32451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wel_32451/07_2026/7wel_32451.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wel_32451/07_2026/7wel_32451.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wel_32451/07_2026/7wel_32451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wel_32451/07_2026/7wel_32451.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wel_32451/07_2026/7wel_32451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wel_32451/07_2026/7wel_32451.map" } resolution = 3.2 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: 6 Type Number sf(0) Gaussians P 21 5.49 5 S 62 5.16 5 Cl 1 4.86 5 C 6594 2.51 5 N 1443 2.21 5 O 1694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9815 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8882 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1102, 8872 Classifications: {'peptide': 1102} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 1069} Chain breaks: 4 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 1102, 8872 Classifications: {'peptide': 1102} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 1069} Chain breaks: 4 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 9083 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 877 Unusual residues: {'95T': 1, 'CLR': 5, 'LPE': 12, 'NAG': 3, 'PCW': 7} Classifications: {'peptide': 2, 'undetermined': 28} Link IDs: {'TRANS': 1, None: 28} Not linked: pdbres="NAG A2001 " pdbres="NAG A2002 " Not linked: pdbres="NAG A2002 " pdbres="NAG A2003 " Not linked: pdbres="NAG A2003 " pdbres="95T A2004 " Not linked: pdbres="95T A2004 " pdbres="CLR A2005 " Not linked: pdbres="CLR A2005 " pdbres="CLR A2006 " ... (remaining 23 not shown) Chain breaks: 1 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 239 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-2': 3} Unresolved non-hydrogen planarities: 7 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A1631 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A1631 " occ=0.50 Time building chain proxies: 3.27, per 1000 atoms: 0.33 Number of scatterers: 9815 At special positions: 0 Unit cell: (130.982, 121.24, 100.672, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 62 16.00 P 21 15.00 O 1694 8.00 N 1443 7.00 C 6594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 319 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 325 " distance=2.03 Simple disulfide: pdb=" SG CYS A 857 " - pdb=" SG CYS A 866 " distance=2.03 Simple disulfide: pdb=" SG CYS A1310 " - pdb=" SG CYS A1332 " distance=2.03 Simple disulfide: pdb=" SG CYS A1678 " - pdb=" SG CYS A1692 " distance=2.22 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A2001 " - " ASN A 819 " " NAG A2002 " - " ASN A 312 " " NAG A2003 " - " ASN A1312 " " NAG B 1 " - " ASN A1328 " " NAG C 1 " - " ASN A1336 " Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 689.1 milliseconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 2 sheets defined 77.7% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 129 through 149 Processing helix chain 'A' and resid 155 through 177 removed outlier: 3.584A pdb=" N ILE A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 212 through 228 removed outlier: 4.354A pdb=" N THR A 216 " --> pdb=" O SER A 212 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 220 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG A 221 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 269 removed outlier: 3.569A pdb=" N ILE A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 255 " --> pdb=" O ILE A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 355 Processing helix chain 'A' and resid 357 through 370 removed outlier: 3.941A pdb=" N LEU A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 407 removed outlier: 3.531A pdb=" N LEU A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 662 Processing helix chain 'A' and resid 664 through 683 removed outlier: 3.721A pdb=" N GLU A 668 " --> pdb=" O ASP A 664 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 670 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 717 removed outlier: 3.558A pdb=" N ILE A 717 " --> pdb=" O VAL A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'A' and resid 727 through 746 removed outlier: 3.675A pdb=" N ILE A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 766 removed outlier: 3.537A pdb=" N PHE A 758 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG A 759 " --> pdb=" O ARG A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 785 Processing helix chain 'A' and resid 787 through 810 removed outlier: 3.601A pdb=" N THR A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 816 Processing helix chain 'A' and resid 816 through 821 removed outlier: 4.240A pdb=" N ILE A 820 " --> pdb=" O ASN A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 847 Processing helix chain 'A' and resid 850 through 859 Processing helix chain 'A' and resid 862 through 893 Processing helix chain 'A' and resid 1137 through 1151 Processing helix chain 'A' and resid 1151 through 1169 removed outlier: 3.613A pdb=" N GLU A1155 " --> pdb=" O HIS A1151 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A1169 " --> pdb=" O SER A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1172 No H-bonds generated for 'chain 'A' and resid 1170 through 1172' Processing helix chain 'A' and resid 1175 through 1178 Processing helix chain 'A' and resid 1179 through 1209 removed outlier: 3.564A pdb=" N LYS A1183 " --> pdb=" O LYS A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1214 Processing helix chain 'A' and resid 1218 through 1238 Processing helix chain 'A' and resid 1245 through 1250 Processing helix chain 'A' and resid 1251 through 1256 removed outlier: 3.616A pdb=" N ALA A1254 " --> pdb=" O THR A1251 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A1255 " --> pdb=" O LEU A1252 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A1256 " --> pdb=" O ARG A1253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1251 through 1256' Processing helix chain 'A' and resid 1257 through 1264 Processing helix chain 'A' and resid 1264 through 1304 Proline residue: A1279 - end of helix removed outlier: 3.558A pdb=" N ASN A1283 " --> pdb=" O PRO A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1335 removed outlier: 3.754A pdb=" N LYS A1333 " --> pdb=" O LYS A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1366 removed outlier: 3.537A pdb=" N LEU A1358 " --> pdb=" O ALA A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1368 through 1378 removed outlier: 3.751A pdb=" N ILE A1372 " --> pdb=" O GLY A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1393 No H-bonds generated for 'chain 'A' and resid 1391 through 1393' Processing helix chain 'A' and resid 1394 through 1429 removed outlier: 3.693A pdb=" N PHE A1398 " --> pdb=" O MET A1394 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY A1406 " --> pdb=" O ILE A1402 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE A1407 " --> pdb=" O ILE A1403 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A1411 " --> pdb=" O PHE A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1452 removed outlier: 3.509A pdb=" N GLY A1450 " --> pdb=" O MET A1446 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A1451 " --> pdb=" O LYS A1447 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS A1452 " --> pdb=" O LYS A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1475 removed outlier: 4.182A pdb=" N ARG A1475 " --> pdb=" O ASP A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1495 removed outlier: 3.809A pdb=" N ASP A1479 " --> pdb=" O ARG A1475 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A1495 " --> pdb=" O ILE A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1501 through 1530 Processing helix chain 'A' and resid 1532 through 1537 Processing helix chain 'A' and resid 1537 through 1564 removed outlier: 3.558A pdb=" N ALA A1558 " --> pdb=" O LEU A1554 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A1561 " --> pdb=" O SER A1557 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1576 removed outlier: 4.195A pdb=" N PHE A1572 " --> pdb=" O SER A1568 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A1574 " --> pdb=" O THR A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1585 removed outlier: 3.589A pdb=" N ILE A1583 " --> pdb=" O ARG A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1586 through 1589 Processing helix chain 'A' and resid 1590 through 1629 Proline residue: A1605 - end of helix removed outlier: 3.569A pdb=" N ASN A1609 " --> pdb=" O PRO A1605 " (cutoff:3.500A) Processing helix chain 'A' and resid 1646 through 1659 removed outlier: 4.063A pdb=" N THR A1659 " --> pdb=" O PHE A1655 " (cutoff:3.500A) Processing helix chain 'A' and resid 1662 through 1671 removed outlier: 3.608A pdb=" N LEU A1666 " --> pdb=" O GLY A1662 " (cutoff:3.500A) Proline residue: A1669 - end of helix Processing helix chain 'A' and resid 1694 through 1728 Processing sheet with id=AA1, first strand: chain 'A' and resid 274 through 278 Processing sheet with id=AA2, first strand: chain 'A' and resid 1318 through 1320 612 hydrogen bonds defined for protein. 1800 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: 1.35 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1374 1.30 - 1.43: 2605 1.43 - 1.56: 5900 1.56 - 1.68: 54 1.68 - 1.81: 103 Bond restraints: 10036 Sorted by residual: bond pdb=" C38 P5S A2029 " pdb=" O37 P5S A2029 " ideal model delta sigma weight residual 1.331 1.465 -0.134 2.00e-02 2.50e+03 4.47e+01 bond pdb=" C11 PCW A2008 " pdb=" O3 PCW A2008 " ideal model delta sigma weight residual 1.326 1.456 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C17 P5S A2029 " pdb=" O19 P5S A2029 " ideal model delta sigma weight residual 1.328 1.457 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C11 PCW A2012 " pdb=" O3 PCW A2012 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C31 PCW A2008 " pdb=" O2 PCW A2008 " ideal model delta sigma weight residual 1.333 1.459 -0.126 2.00e-02 2.50e+03 3.97e+01 ... (remaining 10031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.07: 13133 4.07 - 8.14: 356 8.14 - 12.21: 51 12.21 - 16.28: 2 16.28 - 20.35: 2 Bond angle restraints: 13544 Sorted by residual: angle pdb=" N GLY A1687 " pdb=" CA GLY A1687 " pdb=" C GLY A1687 " ideal model delta sigma weight residual 112.73 124.33 -11.60 1.20e+00 6.94e-01 9.35e+01 angle pdb=" N LYS A 155 " pdb=" CA LYS A 155 " pdb=" C LYS A 155 " ideal model delta sigma weight residual 114.62 104.44 10.18 1.14e+00 7.69e-01 7.98e+01 angle pdb=" N ASP A1691 " pdb=" CA ASP A1691 " pdb=" C ASP A1691 " ideal model delta sigma weight residual 113.15 103.68 9.47 1.19e+00 7.06e-01 6.33e+01 angle pdb=" N ALA A1589 " pdb=" CA ALA A1589 " pdb=" C ALA A1589 " ideal model delta sigma weight residual 111.36 119.65 -8.29 1.09e+00 8.42e-01 5.79e+01 angle pdb=" C09 95T A2004 " pdb=" C13 95T A2004 " pdb=" N06 95T A2004 " ideal model delta sigma weight residual 119.48 139.83 -20.35 3.00e+00 1.11e-01 4.60e+01 ... (remaining 13539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.52: 5599 32.52 - 65.03: 252 65.03 - 97.55: 22 97.55 - 130.06: 6 130.06 - 162.58: 6 Dihedral angle restraints: 5885 sinusoidal: 2662 harmonic: 3223 Sorted by residual: dihedral pdb=" CB CYS A 310 " pdb=" SG CYS A 310 " pdb=" SG CYS A 325 " pdb=" CB CYS A 325 " ideal model delta sinusoidal sigma weight residual -86.00 -171.70 85.70 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS A 857 " pdb=" SG CYS A 857 " pdb=" SG CYS A 866 " pdb=" CB CYS A 866 " ideal model delta sinusoidal sigma weight residual 93.00 176.32 -83.32 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" N PHE A1408 " pdb=" C PHE A1408 " pdb=" CA PHE A1408 " pdb=" CB PHE A1408 " ideal model delta harmonic sigma weight residual 122.80 141.40 -18.60 0 2.50e+00 1.60e-01 5.53e+01 ... (remaining 5882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 1450 0.152 - 0.304: 67 0.304 - 0.457: 6 0.457 - 0.609: 1 0.609 - 0.761: 1 Chirality restraints: 1525 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.23e+01 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.55e+01 chirality pdb=" CA PHE A1408 " pdb=" N PHE A1408 " pdb=" C PHE A1408 " pdb=" CB PHE A1408 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.45e+01 ... (remaining 1522 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.300 2.00e-02 2.50e+03 2.64e-01 8.74e+02 pdb=" C7 NAG B 1 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.098 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.475 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.276 2.00e-02 2.50e+03 2.31e-01 6.68e+02 pdb=" C7 NAG C 1 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.183 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.390 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.244 2.00e-02 2.50e+03 2.09e-01 5.48e+02 pdb=" C7 NAG B 2 " -0.051 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.027 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.350 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.184 2.00e-02 2.50e+03 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 10 2.46 - 3.07: 6832 3.07 - 3.68: 14149 3.68 - 4.29: 21411 4.29 - 4.90: 34858 Nonbonded interactions: 77260 Sorted by model distance: nonbonded pdb=" CD2 LEU A 214 " pdb=" NH2 ARG A 215 " model vdw 1.853 3.540 nonbonded pdb=" O3 NAG A2001 " pdb=" O7 NAG A2001 " model vdw 2.129 3.040 nonbonded pdb=" CD2 LEU A 889 " pdb=" OD1 ASN A1411 " model vdw 2.279 3.460 nonbonded pdb=" CD1 PHE A1171 " pdb=" C2N LPE A2022 " model vdw 2.383 3.760 nonbonded pdb=" O GLN A1500 " pdb=" O1P PCW A2027 " model vdw 2.383 3.040 ... (remaining 77255 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 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.890 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 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 : 0.010 0.190 10048 Z= 0.535 Angle : 1.488 20.516 13575 Z= 0.739 Chirality : 0.073 0.761 1525 Planarity : 0.013 0.264 1549 Dihedral : 18.127 162.577 3782 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 23.36 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.03 % Favored : 95.42 % Rotamer: Outliers : 0.41 % Allowed : 2.16 % Favored : 97.43 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.26), residues: 1095 helix: 1.56 (0.19), residues: 793 sheet: -1.42 (0.97), residues: 12 loop : -1.69 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 756 TYR 0.056 0.003 TYR A1374 PHE 0.047 0.002 PHE A 135 TRP 0.077 0.002 TRP A1369 HIS 0.002 0.001 HIS A 833 Details of bonding type rmsd/Z covalent geometry : bond 0.00971 / 0.52 (10036) covalent geometry : angle 1.45356 / 0.73 (13544) SS BOND : bond 0.08481 / 6.23 ( 5) SS BOND : angle 4.70055 / 4.48 ( 10) hydrogen bonds : bond 0.15879 / 10.78 ( 612) hydrogen bonds : angle 6.43482 / 4.82 ( 1800) link_BETA1-4 : bond 0.01304 / 0.69 ( 2) link_BETA1-4 : angle 3.20903 / 2.51 ( 6) link_NAG-ASN : bond 0.04499 / 2.36 ( 5) link_NAG-ASN : angle 8.84986 / 6.69 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 202 time to evaluate : 0.226 Fit side-chains REVERT: A 1160 PHE cc_start: 0.8306 (m-80) cc_final: 0.8105 (m-80) REVERT: A 1215 THR cc_start: 0.7703 (m) cc_final: 0.7459 (p) REVERT: A 1446 MET cc_start: 0.6689 (ttp) cc_final: 0.6464 (ttp) outliers start: 4 outliers final: 1 residues processed: 204 average time/residue: 0.0747 time to fit residues: 22.1900 Evaluate side-chains 141 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 ASN A 190 ASN A 701 ASN A 833 HIS A 837 HIS A1216 ASN ** A1362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1631 HIS A Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.141854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.115859 restraints weight = 35436.887| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.02 r_work: 0.3373 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 10048 Z= 0.154 Angle : 0.744 15.143 13575 Z= 0.357 Chirality : 0.043 0.289 1525 Planarity : 0.005 0.048 1549 Dihedral : 19.164 171.678 1741 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.39 % Favored : 96.34 % Rotamer: Outliers : 1.54 % Allowed : 7.91 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.26), residues: 1095 helix: 1.72 (0.18), residues: 795 sheet: -1.96 (1.18), residues: 12 loop : -1.21 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 756 TYR 0.037 0.003 TYR A1374 PHE 0.040 0.002 PHE A1556 TRP 0.039 0.001 TRP A1369 HIS 0.003 0.001 HIS A1151 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (10036) covalent geometry : angle 0.72600 / 0.35 (13544) SS BOND : bond 0.00534 / 0.33 ( 5) SS BOND : angle 1.99933 / 1.59 ( 10) hydrogen bonds : bond 0.05302 / 3.55 ( 612) hydrogen bonds : angle 4.52824 / 3.33 ( 1800) link_BETA1-4 : bond 0.00356 / 0.17 ( 2) link_BETA1-4 : angle 2.61942 / 1.89 ( 6) link_NAG-ASN : bond 0.00651 / 0.33 ( 5) link_NAG-ASN : angle 4.50002 / 3.16 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.231 Fit side-chains REVERT: A 1215 THR cc_start: 0.8253 (m) cc_final: 0.8005 (p) outliers start: 15 outliers final: 9 residues processed: 157 average time/residue: 0.0740 time to fit residues: 18.0607 Evaluate side-chains 148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1252 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 44 optimal weight: 0.1980 chunk 51 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1362 GLN A1631 HIS B Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.142127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.116865 restraints weight = 28672.632| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.66 r_work: 0.3391 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10048 Z= 0.129 Angle : 0.648 13.601 13575 Z= 0.313 Chirality : 0.040 0.293 1525 Planarity : 0.005 0.045 1549 Dihedral : 17.258 174.575 1739 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.39 % Favored : 96.25 % Rotamer: Outliers : 1.13 % Allowed : 10.48 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.26), residues: 1095 helix: 1.86 (0.18), residues: 795 sheet: -2.34 (1.13), residues: 12 loop : -1.00 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1309 TYR 0.026 0.002 TYR A1374 PHE 0.045 0.002 PHE A1556 TRP 0.034 0.001 TRP A1369 HIS 0.003 0.001 HIS A 837 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (10036) covalent geometry : angle 0.63550 / 0.31 (13544) SS BOND : bond 0.00388 / 0.19 ( 5) SS BOND : angle 1.59667 / 1.36 ( 10) hydrogen bonds : bond 0.04507 / 3.00 ( 612) hydrogen bonds : angle 4.25668 / 3.13 ( 1800) link_BETA1-4 : bond 0.00452 / 0.22 ( 2) link_BETA1-4 : angle 1.79878 / 1.29 ( 6) link_NAG-ASN : bond 0.00372 / 0.19 ( 5) link_NAG-ASN : angle 3.45327 / 2.41 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.370 Fit side-chains REVERT: A 218 ARG cc_start: 0.7481 (ttm170) cc_final: 0.7249 (ttm-80) REVERT: A 1215 THR cc_start: 0.8177 (m) cc_final: 0.7922 (p) REVERT: A 1556 PHE cc_start: 0.8002 (t80) cc_final: 0.7762 (t80) outliers start: 11 outliers final: 6 residues processed: 151 average time/residue: 0.0737 time to fit residues: 17.1321 Evaluate side-chains 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 1446 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 65 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.141192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.117672 restraints weight = 18802.784| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.11 r_work: 0.3423 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10048 Z= 0.125 Angle : 0.608 11.902 13575 Z= 0.296 Chirality : 0.039 0.233 1525 Planarity : 0.005 0.046 1549 Dihedral : 16.040 174.918 1739 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.39 % Favored : 96.25 % Rotamer: Outliers : 1.03 % Allowed : 11.20 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.26), residues: 1095 helix: 1.88 (0.18), residues: 794 sheet: -2.38 (1.10), residues: 12 loop : -0.77 (0.40), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 756 TYR 0.023 0.002 TYR A1374 PHE 0.043 0.002 PHE A1556 TRP 0.021 0.001 TRP A1369 HIS 0.002 0.001 HIS A1151 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (10036) covalent geometry : angle 0.59817 / 0.29 (13544) SS BOND : bond 0.00356 / 0.18 ( 5) SS BOND : angle 1.43621 / 1.20 ( 10) hydrogen bonds : bond 0.04252 / 2.84 ( 612) hydrogen bonds : angle 4.09719 / 3.01 ( 1800) link_BETA1-4 : bond 0.00292 / 0.14 ( 2) link_BETA1-4 : angle 1.82084 / 1.29 ( 6) link_NAG-ASN : bond 0.00402 / 0.21 ( 5) link_NAG-ASN : angle 3.00669 / 2.31 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.275 Fit side-chains REVERT: A 1215 THR cc_start: 0.8437 (m) cc_final: 0.8161 (p) REVERT: A 1446 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6889 (mtm) REVERT: A 1556 PHE cc_start: 0.8152 (t80) cc_final: 0.7945 (t80) outliers start: 10 outliers final: 6 residues processed: 155 average time/residue: 0.0642 time to fit residues: 15.3748 Evaluate side-chains 147 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1713 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 68 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 43 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.0370 chunk 58 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.141564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.117101 restraints weight = 24252.995| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.44 r_work: 0.3401 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10048 Z= 0.114 Angle : 0.587 11.098 13575 Z= 0.285 Chirality : 0.037 0.185 1525 Planarity : 0.004 0.045 1549 Dihedral : 15.394 175.961 1739 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.37 % Allowed : 3.66 % Favored : 95.97 % Rotamer: Outliers : 1.13 % Allowed : 12.54 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.26), residues: 1095 helix: 1.95 (0.18), residues: 791 sheet: -2.59 (1.09), residues: 12 loop : -0.74 (0.40), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1309 TYR 0.020 0.002 TYR A1374 PHE 0.034 0.001 PHE A1556 TRP 0.015 0.001 TRP A1369 HIS 0.002 0.001 HIS A 837 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (10036) covalent geometry : angle 0.57909 / 0.28 (13544) SS BOND : bond 0.00308 / 0.16 ( 5) SS BOND : angle 1.22382 / 1.06 ( 10) hydrogen bonds : bond 0.04021 / 2.68 ( 612) hydrogen bonds : angle 4.03807 / 2.97 ( 1800) link_BETA1-4 : bond 0.00368 / 0.18 ( 2) link_BETA1-4 : angle 1.43016 / 1.01 ( 6) link_NAG-ASN : bond 0.00369 / 0.19 ( 5) link_NAG-ASN : angle 2.70276 / 2.11 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.374 Fit side-chains REVERT: A 324 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.7453 (tt) REVERT: A 390 ASN cc_start: 0.7985 (t0) cc_final: 0.7649 (m-40) REVERT: A 684 MET cc_start: 0.8946 (ttm) cc_final: 0.8736 (mtm) REVERT: A 1215 THR cc_start: 0.8149 (m) cc_final: 0.7870 (p) REVERT: A 1446 MET cc_start: 0.6982 (OUTLIER) cc_final: 0.6662 (mtm) REVERT: A 1556 PHE cc_start: 0.8088 (t80) cc_final: 0.7871 (t80) REVERT: A 1679 ASP cc_start: 0.7656 (t0) cc_final: 0.6992 (t0) outliers start: 11 outliers final: 4 residues processed: 154 average time/residue: 0.0717 time to fit residues: 17.2667 Evaluate side-chains 149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1713 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 2 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.137376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.112398 restraints weight = 25874.197| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.51 r_work: 0.3339 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10048 Z= 0.153 Angle : 0.623 10.742 13575 Z= 0.307 Chirality : 0.039 0.172 1525 Planarity : 0.005 0.046 1549 Dihedral : 15.068 176.187 1739 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.57 % Favored : 96.15 % Rotamer: Outliers : 1.75 % Allowed : 13.26 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.26), residues: 1095 helix: 1.82 (0.18), residues: 790 sheet: -3.22 (1.06), residues: 14 loop : -0.87 (0.40), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1309 TYR 0.021 0.002 TYR A1374 PHE 0.033 0.002 PHE A1556 TRP 0.016 0.001 TRP A1369 HIS 0.003 0.001 HIS A 837 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (10036) covalent geometry : angle 0.61514 / 0.30 (13544) SS BOND : bond 0.00541 / 0.27 ( 5) SS BOND : angle 1.24372 / 1.04 ( 10) hydrogen bonds : bond 0.04617 / 3.08 ( 612) hydrogen bonds : angle 4.13141 / 3.02 ( 1800) link_BETA1-4 : bond 0.00346 / 0.17 ( 2) link_BETA1-4 : angle 1.57771 / 1.12 ( 6) link_NAG-ASN : bond 0.00353 / 0.18 ( 5) link_NAG-ASN : angle 2.73184 / 2.14 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.250 Fit side-chains REVERT: A 390 ASN cc_start: 0.8157 (t0) cc_final: 0.7796 (m-40) REVERT: A 713 VAL cc_start: 0.8637 (OUTLIER) cc_final: 0.8427 (p) REVERT: A 826 ASP cc_start: 0.7739 (p0) cc_final: 0.7313 (t0) REVERT: A 1215 THR cc_start: 0.8309 (m) cc_final: 0.8037 (p) REVERT: A 1446 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6704 (mtm) REVERT: A 1679 ASP cc_start: 0.7892 (t0) cc_final: 0.7474 (t70) outliers start: 17 outliers final: 10 residues processed: 153 average time/residue: 0.0792 time to fit residues: 18.3760 Evaluate side-chains 152 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1603 SER Chi-restraints excluded: chain A residue 1713 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 105 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.138265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.113218 restraints weight = 28148.696| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.56 r_work: 0.3352 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10048 Z= 0.129 Angle : 0.594 10.278 13575 Z= 0.293 Chirality : 0.038 0.163 1525 Planarity : 0.004 0.045 1549 Dihedral : 14.785 176.829 1739 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.39 % Favored : 96.34 % Rotamer: Outliers : 1.13 % Allowed : 13.98 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.26), residues: 1095 helix: 1.81 (0.18), residues: 792 sheet: -2.70 (1.13), residues: 12 loop : -0.72 (0.40), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 762 TYR 0.025 0.002 TYR A1705 PHE 0.027 0.001 PHE A1421 TRP 0.026 0.001 TRP A1369 HIS 0.002 0.001 HIS A 837 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (10036) covalent geometry : angle 0.58732 / 0.29 (13544) SS BOND : bond 0.00437 / 0.22 ( 5) SS BOND : angle 1.04386 / 0.89 ( 10) hydrogen bonds : bond 0.04306 / 2.87 ( 612) hydrogen bonds : angle 4.10022 / 3.01 ( 1800) link_BETA1-4 : bond 0.00398 / 0.20 ( 2) link_BETA1-4 : angle 1.26003 / 0.89 ( 6) link_NAG-ASN : bond 0.00363 / 0.19 ( 5) link_NAG-ASN : angle 2.60062 / 2.05 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.341 Fit side-chains REVERT: A 390 ASN cc_start: 0.8124 (t0) cc_final: 0.7782 (m-40) REVERT: A 684 MET cc_start: 0.8906 (ttm) cc_final: 0.8699 (mtm) REVERT: A 826 ASP cc_start: 0.7739 (p0) cc_final: 0.7381 (t0) REVERT: A 1215 THR cc_start: 0.8220 (m) cc_final: 0.7955 (p) REVERT: A 1446 MET cc_start: 0.6978 (OUTLIER) cc_final: 0.6670 (mtm) REVERT: A 1679 ASP cc_start: 0.7990 (t0) cc_final: 0.7559 (t70) outliers start: 11 outliers final: 7 residues processed: 148 average time/residue: 0.0700 time to fit residues: 16.1832 Evaluate side-chains 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1603 SER Chi-restraints excluded: chain A residue 1713 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 0.0050 chunk 37 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1151 HIS A1420 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.137113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.112063 restraints weight = 27802.729| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.59 r_work: 0.3331 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10048 Z= 0.145 Angle : 0.614 10.085 13575 Z= 0.304 Chirality : 0.039 0.166 1525 Planarity : 0.004 0.045 1549 Dihedral : 14.595 177.598 1739 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.85 % Favored : 95.88 % Rotamer: Outliers : 1.34 % Allowed : 13.87 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.26), residues: 1095 helix: 1.75 (0.18), residues: 793 sheet: -3.22 (1.10), residues: 14 loop : -0.79 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 215 TYR 0.024 0.002 TYR A1705 PHE 0.030 0.002 PHE A1421 TRP 0.024 0.001 TRP A1369 HIS 0.003 0.001 HIS A1151 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (10036) covalent geometry : angle 0.60745 / 0.30 (13544) SS BOND : bond 0.00548 / 0.27 ( 5) SS BOND : angle 1.09435 / 0.93 ( 10) hydrogen bonds : bond 0.04452 / 2.97 ( 612) hydrogen bonds : angle 4.13496 / 3.02 ( 1800) link_BETA1-4 : bond 0.00348 / 0.18 ( 2) link_BETA1-4 : angle 1.29079 / 0.90 ( 6) link_NAG-ASN : bond 0.00349 / 0.19 ( 5) link_NAG-ASN : angle 2.54886 / 2.04 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.230 Fit side-chains REVERT: A 390 ASN cc_start: 0.8115 (t0) cc_final: 0.7805 (m-40) REVERT: A 684 MET cc_start: 0.8931 (ttm) cc_final: 0.8704 (mtm) REVERT: A 826 ASP cc_start: 0.7794 (p0) cc_final: 0.7527 (t0) REVERT: A 1215 THR cc_start: 0.8273 (m) cc_final: 0.8000 (p) REVERT: A 1446 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6641 (mtm) REVERT: A 1679 ASP cc_start: 0.8188 (t0) cc_final: 0.7743 (t70) outliers start: 13 outliers final: 10 residues processed: 148 average time/residue: 0.0619 time to fit residues: 14.4522 Evaluate side-chains 150 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1603 SER Chi-restraints excluded: chain A residue 1713 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 39 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 0.0770 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1151 HIS A1489 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.138547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.114553 restraints weight = 22236.781| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.26 r_work: 0.3380 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10048 Z= 0.124 Angle : 0.586 9.897 13575 Z= 0.291 Chirality : 0.038 0.156 1525 Planarity : 0.004 0.045 1549 Dihedral : 14.352 178.701 1739 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.48 % Favored : 96.25 % Rotamer: Outliers : 0.92 % Allowed : 14.18 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.26), residues: 1095 helix: 1.83 (0.18), residues: 793 sheet: -2.47 (1.17), residues: 12 loop : -0.72 (0.40), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 762 TYR 0.032 0.002 TYR A1705 PHE 0.031 0.001 PHE A1421 TRP 0.020 0.001 TRP A1369 HIS 0.002 0.001 HIS A 837 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (10036) covalent geometry : angle 0.58009 / 0.29 (13544) SS BOND : bond 0.00429 / 0.21 ( 5) SS BOND : angle 0.99185 / 0.85 ( 10) hydrogen bonds : bond 0.04161 / 2.78 ( 612) hydrogen bonds : angle 4.07463 / 2.98 ( 1800) link_BETA1-4 : bond 0.00331 / 0.17 ( 2) link_BETA1-4 : angle 1.06217 / 0.74 ( 6) link_NAG-ASN : bond 0.00356 / 0.19 ( 5) link_NAG-ASN : angle 2.38863 / 1.93 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 0.349 Fit side-chains REVERT: A 147 MET cc_start: 0.8693 (mtm) cc_final: 0.8460 (ptp) REVERT: A 390 ASN cc_start: 0.8068 (t0) cc_final: 0.7749 (m-40) REVERT: A 684 MET cc_start: 0.8867 (ttm) cc_final: 0.8651 (mtm) REVERT: A 713 VAL cc_start: 0.8670 (p) cc_final: 0.8468 (p) REVERT: A 826 ASP cc_start: 0.7763 (p0) cc_final: 0.7540 (t0) REVERT: A 1215 THR cc_start: 0.8157 (m) cc_final: 0.7885 (p) REVERT: A 1446 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.6637 (mtm) REVERT: A 1587 ILE cc_start: 0.9009 (pt) cc_final: 0.8579 (mt) REVERT: A 1679 ASP cc_start: 0.8157 (t0) cc_final: 0.7747 (t70) outliers start: 9 outliers final: 8 residues processed: 153 average time/residue: 0.0742 time to fit residues: 17.8551 Evaluate side-chains 152 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1603 SER Chi-restraints excluded: chain A residue 1713 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 68 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1151 HIS A1216 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.138772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114182 restraints weight = 23948.739| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.39 r_work: 0.3370 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10048 Z= 0.123 Angle : 0.596 10.043 13575 Z= 0.295 Chirality : 0.038 0.158 1525 Planarity : 0.004 0.045 1549 Dihedral : 14.148 179.508 1739 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.57 % Favored : 96.15 % Rotamer: Outliers : 1.34 % Allowed : 14.29 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.26), residues: 1095 helix: 1.88 (0.18), residues: 790 sheet: -2.30 (1.20), residues: 12 loop : -0.66 (0.40), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 762 TYR 0.029 0.002 TYR A1705 PHE 0.031 0.001 PHE A1421 TRP 0.020 0.001 TRP A1369 HIS 0.002 0.001 HIS A 837 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10036) covalent geometry : angle 0.58738 / 0.29 (13544) SS BOND : bond 0.00404 / 0.20 ( 5) SS BOND : angle 0.95223 / 0.80 ( 10) hydrogen bonds : bond 0.04089 / 2.72 ( 612) hydrogen bonds : angle 4.06345 / 2.97 ( 1800) link_BETA1-4 : bond 0.00370 / 0.19 ( 2) link_BETA1-4 : angle 0.95958 / 0.82 ( 6) link_NAG-ASN : bond 0.00424 / 0.22 ( 5) link_NAG-ASN : angle 3.00147 / 2.20 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.268 Fit side-chains REVERT: A 147 MET cc_start: 0.8749 (mtm) cc_final: 0.8532 (ptp) REVERT: A 390 ASN cc_start: 0.8063 (t0) cc_final: 0.7739 (m-40) REVERT: A 684 MET cc_start: 0.8922 (ttm) cc_final: 0.8687 (mtm) REVERT: A 826 ASP cc_start: 0.7859 (p0) cc_final: 0.7567 (t0) REVERT: A 1215 THR cc_start: 0.8192 (m) cc_final: 0.7904 (p) REVERT: A 1446 MET cc_start: 0.6933 (OUTLIER) cc_final: 0.6624 (mtm) REVERT: A 1587 ILE cc_start: 0.9012 (pt) cc_final: 0.8605 (mt) REVERT: A 1679 ASP cc_start: 0.8188 (t0) cc_final: 0.7763 (t70) outliers start: 13 outliers final: 10 residues processed: 151 average time/residue: 0.0674 time to fit residues: 15.9561 Evaluate side-chains 156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 1446 MET Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1603 SER Chi-restraints excluded: chain A residue 1713 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 5 optimal weight: 0.0670 chunk 94 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.0970 chunk 74 optimal weight: 0.0070 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 overall best weight: 0.2134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1151 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.142459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.117218 restraints weight = 29034.241| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.71 r_work: 0.3406 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10048 Z= 0.107 Angle : 0.565 9.928 13575 Z= 0.280 Chirality : 0.037 0.188 1525 Planarity : 0.004 0.044 1549 Dihedral : 13.534 178.500 1739 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.48 % Favored : 96.25 % Rotamer: Outliers : 0.82 % Allowed : 14.90 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.27), residues: 1095 helix: 2.00 (0.18), residues: 789 sheet: -2.07 (1.18), residues: 12 loop : -0.60 (0.41), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 762 TYR 0.027 0.002 TYR A1705 PHE 0.030 0.001 PHE A1421 TRP 0.019 0.001 TRP A1369 HIS 0.001 0.000 HIS A 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (10036) covalent geometry : angle 0.55840 / 0.28 (13544) SS BOND : bond 0.00232 / 0.12 ( 5) SS BOND : angle 0.89619 / 0.77 ( 10) hydrogen bonds : bond 0.03607 / 2.40 ( 612) hydrogen bonds : angle 3.95759 / 2.90 ( 1800) link_BETA1-4 : bond 0.00439 / 0.22 ( 2) link_BETA1-4 : angle 0.91051 / 0.71 ( 6) link_NAG-ASN : bond 0.00414 / 0.22 ( 5) link_NAG-ASN : angle 2.52578 / 1.92 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2371.16 seconds wall clock time: 41 minutes 25.50 seconds (2485.50 seconds total)