Starting phenix.real_space_refine on Thu Jul 2 22:19:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wfr_32475/07_2026/7wfr_32475.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wfr_32475/07_2026/7wfr_32475.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wfr_32475/07_2026/7wfr_32475.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wfr_32475/07_2026/7wfr_32475.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wfr_32475/07_2026/7wfr_32475.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wfr_32475/07_2026/7wfr_32475.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wfr_32475/07_2026/7wfr_32475.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wfr_32475/07_2026/7wfr_32475.cif" } resolution = 3.0 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 20 5.49 5 S 62 5.16 5 Cl 1 4.86 5 C 6545 2.51 5 N 1438 2.21 5 O 1682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 121 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: 9748 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8861 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1100, 8851 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 1067} 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: 1100, 8851 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 1067} 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: 9060 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: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 831 Unusual residues: {'95T': 1, 'CLR': 5, 'LPE': 12, 'NAG': 3, 'PCW': 7} Classifications: {'peptide': 1, 'undetermined': 28} Link IDs: {None: 28} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-4': 1, 'PCW:plan-2': 3} Unresolved non-hydrogen planarities: 8 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: 3.22, per 1000 atoms: 0.33 Number of scatterers: 9748 At special positions: 0 Unit cell: (129.9, 124.487, 101.755, 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 20 15.00 O 1682 8.00 N 1438 7.00 C 6545 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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: 1.00 Conformation dependent library (CDL) restraints added in 690.6 milliseconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2082 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 2 sheets defined 75.2% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 130 through 149 removed outlier: 3.773A pdb=" N LEU A 141 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A 147 " --> pdb=" O ASN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 175 removed outlier: 3.957A pdb=" N ILE A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS A 171 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 205 removed outlier: 3.551A pdb=" N THR A 198 " --> pdb=" O PHE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 220 removed outlier: 3.993A pdb=" N PHE A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 229 removed outlier: 3.687A pdb=" N SER A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 246 removed outlier: 3.675A pdb=" N ILE A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 269 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 341 through 354 Processing helix chain 'A' and resid 357 through 370 removed outlier: 4.137A pdb=" N LEU A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 removed outlier: 4.023A pdb=" N PHE A 377 " --> pdb=" O TYR A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 407 removed outlier: 3.684A pdb=" N GLN A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN A 404 " --> pdb=" O TYR A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 662 Processing helix chain 'A' and resid 665 through 683 removed outlier: 3.502A pdb=" N LEU A 669 " --> pdb=" O PRO A 665 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR A 670 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 671 " --> pdb=" O ALA A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 717 Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'A' and resid 727 through 746 removed outlier: 3.749A pdb=" N ILE A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE A 732 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 757 Processing helix chain 'A' and resid 758 through 766 removed outlier: 3.598A pdb=" N ARG A 762 " --> pdb=" O ARG A 759 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE A 764 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 783 Processing helix chain 'A' and resid 787 through 816 removed outlier: 3.661A pdb=" N THR A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLU A 811 " --> pdb=" O GLN A 807 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASN A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 847 Processing helix chain 'A' and resid 850 through 861 Processing helix chain 'A' and resid 862 through 894 Processing helix chain 'A' and resid 1137 through 1150 Processing helix chain 'A' and resid 1151 through 1168 Processing helix chain 'A' and resid 1169 through 1172 Processing helix chain 'A' and resid 1179 through 1209 removed outlier: 3.716A pdb=" N LYS A1183 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A1184 " --> pdb=" O PRO A1180 " (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 1243 through 1251 removed outlier: 3.763A pdb=" N THR A1251 " --> pdb=" O LYS A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1260 Proline residue: A1257 - end of helix Processing helix chain 'A' and resid 1264 through 1304 Proline residue: A1279 - end of helix Processing helix chain 'A' and resid 1328 through 1335 Processing helix chain 'A' and resid 1352 through 1365 Processing helix chain 'A' and resid 1368 through 1378 removed outlier: 3.851A 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 1406 removed outlier: 3.868A pdb=" N PHE A1398 " --> pdb=" O MET A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1428 Processing helix chain 'A' and resid 1436 through 1451 removed outlier: 3.835A pdb=" N SER A1451 " --> pdb=" O LYS A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1474 removed outlier: 3.979A pdb=" N VAL A1469 " --> pdb=" O PHE A1465 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A1470 " --> pdb=" O GLN A1466 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1495 removed outlier: 3.967A pdb=" N ASP A1479 " --> pdb=" O ARG A1475 " (cutoff:3.500A) Processing helix chain 'A' and resid 1501 through 1530 removed outlier: 3.807A pdb=" N THR A1505 " --> pdb=" O SER A1501 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1561 removed outlier: 3.556A pdb=" N VAL A1541 " --> pdb=" O ASN A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1576 removed outlier: 4.234A pdb=" N PHE A1572 " --> pdb=" O SER A1568 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A1573 " --> pdb=" O PRO A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1585 removed outlier: 3.800A 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 Processing helix chain 'A' and resid 1646 through 1659 removed outlier: 4.216A pdb=" N THR A1659 " --> pdb=" O PHE A1655 " (cutoff:3.500A) Processing helix chain 'A' and resid 1662 through 1671 removed outlier: 3.501A 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 removed outlier: 3.615A pdb=" N ILE A1707 " --> pdb=" O THR A1703 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A1715 " --> pdb=" O LEU A1711 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A1723 " --> pdb=" O ALA A1719 " (cutoff:3.500A) 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 1309 through 1312 579 hydrogen bonds defined for protein. 1707 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: 1.13 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1569 1.33 - 1.45: 2599 1.45 - 1.57: 5656 1.57 - 1.70: 41 1.70 - 1.82: 103 Bond restraints: 9968 Sorted by residual: bond pdb=" C11 PCW A2007 " pdb=" O3 PCW A2007 " ideal model delta sigma weight residual 1.326 1.459 -0.133 2.00e-02 2.50e+03 4.40e+01 bond pdb=" C11 PCW A2019 " pdb=" O3 PCW A2019 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C11 PCW A2013 " pdb=" O3 PCW A2013 " ideal model delta sigma weight residual 1.326 1.454 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C11 PCW A2016 " pdb=" O3 PCW A2016 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C31 PCW A2007 " pdb=" O2 PCW A2007 " ideal model delta sigma weight residual 1.333 1.457 -0.124 2.00e-02 2.50e+03 3.86e+01 ... (remaining 9963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.03: 13231 5.03 - 10.06: 215 10.06 - 15.08: 12 15.08 - 20.11: 0 20.11 - 25.14: 3 Bond angle restraints: 13461 Sorted by residual: angle pdb=" N ALA A 205 " pdb=" CA ALA A 205 " pdb=" C ALA A 205 " ideal model delta sigma weight residual 111.14 123.54 -12.40 1.08e+00 8.57e-01 1.32e+02 angle pdb=" N VAL A1632 " pdb=" CA VAL A1632 " pdb=" C VAL A1632 " ideal model delta sigma weight residual 110.05 121.50 -11.45 1.09e+00 8.42e-01 1.10e+02 angle pdb=" C5 PCW A2019 " pdb=" N PCW A2019 " pdb=" C8 PCW A2019 " ideal model delta sigma weight residual 111.64 86.50 25.14 3.00e+00 1.11e-01 7.02e+01 angle pdb=" N SER A1685 " pdb=" CA SER A1685 " pdb=" C SER A1685 " ideal model delta sigma weight residual 110.28 121.54 -11.26 1.48e+00 4.57e-01 5.78e+01 angle pdb=" C6 PCW A2019 " pdb=" N PCW A2019 " pdb=" C8 PCW A2019 " ideal model delta sigma weight residual 109.11 86.48 22.63 3.00e+00 1.11e-01 5.69e+01 ... (remaining 13456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.51: 5493 32.51 - 65.02: 321 65.02 - 97.53: 20 97.53 - 130.04: 4 130.04 - 162.55: 8 Dihedral angle restraints: 5846 sinusoidal: 2631 harmonic: 3215 Sorted by residual: 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 93.00 176.85 -83.85 1 1.00e+01 1.00e-02 8.57e+01 dihedral pdb=" CA ASP A1691 " pdb=" C ASP A1691 " pdb=" N CYS A1692 " pdb=" CA CYS A1692 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" N PCW A2006 " pdb=" C4 PCW A2006 " pdb=" C5 PCW A2006 " pdb=" O4P PCW A2006 " ideal model delta sinusoidal sigma weight residual 293.34 130.79 162.55 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 5843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1260 0.073 - 0.146: 209 0.146 - 0.219: 34 0.219 - 0.292: 17 0.292 - 0.365: 1 Chirality restraints: 1521 Sorted by residual: 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 1.62e+01 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 -2.32 -0.08 2.00e-02 2.50e+03 1.52e+01 chirality pdb=" CA ALA A 205 " pdb=" N ALA A 205 " pdb=" C ALA A 205 " pdb=" CB ALA A 205 " both_signs ideal model delta sigma weight residual False 2.48 2.12 0.36 2.00e-01 2.50e+01 3.33e+00 ... (remaining 1518 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " -0.229 2.00e-02 2.50e+03 1.94e-01 4.73e+02 pdb=" C7 NAG B 2 " 0.048 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " 0.320 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C08 95T A2004 " 0.205 2.00e-02 2.50e+03 1.73e-01 3.73e+02 pdb=" C09 95T A2004 " 0.139 2.00e-02 2.50e+03 pdb=" C13 95T A2004 " -0.053 2.00e-02 2.50e+03 pdb=" N06 95T A2004 " -0.291 2.00e-02 2.50e+03 pdb=" O05 95T A2004 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.042 2.00e-02 2.50e+03 3.43e-02 1.47e+01 pdb=" C7 NAG B 1 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.054 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.008 2.00e-02 2.50e+03 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 46 2.54 - 3.13: 7950 3.13 - 3.72: 14563 3.72 - 4.31: 20457 4.31 - 4.90: 33683 Nonbonded interactions: 76699 Sorted by model distance: nonbonded pdb=" O3 NAG A2001 " pdb=" O7 NAG A2001 " model vdw 1.953 3.040 nonbonded pdb=" N GLU A1503 " pdb=" OE1 GLU A1503 " model vdw 2.269 3.120 nonbonded pdb=" O THR A1659 " pdb=" OG SER A1660 " model vdw 2.287 3.040 nonbonded pdb=" OD1 ASP A1664 " pdb=" N GLY A1665 " model vdw 2.343 3.120 nonbonded pdb=" O SER A 357 " pdb=" OG SER A 357 " model vdw 2.359 3.040 ... (remaining 76694 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: 0.910 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.410 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: 0.010 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 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 : 0.009 0.133 9980 Z= 0.487 Angle : 1.398 25.139 13492 Z= 0.668 Chirality : 0.061 0.365 1521 Planarity : 0.008 0.194 1541 Dihedral : 19.770 162.547 3749 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.41 % Favored : 94.50 % Rotamer: Outliers : 0.51 % Allowed : 1.13 % Favored : 98.35 % 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: 0.30 (0.26), residues: 1093 helix: 1.15 (0.19), residues: 753 sheet: -3.27 (0.84), residues: 22 loop : -1.82 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 367 TYR 0.044 0.003 TYR A1717 PHE 0.041 0.002 PHE A 194 TRP 0.026 0.002 TRP A 729 HIS 0.002 0.001 HIS A 824 Details of bonding type rmsd/Z covalent geometry : bond 0.00919 / 0.48 ( 9968) covalent geometry : angle 1.39174 / 0.67 (13461) SS BOND : bond 0.00319 / 0.18 ( 5) SS BOND : angle 2.80494 / 1.64 ( 10) hydrogen bonds : bond 0.16707 / 10.99 ( 579) hydrogen bonds : angle 6.28321 / 4.52 ( 1707) link_BETA1-4 : bond 0.00167 / 0.09 ( 2) link_BETA1-4 : angle 0.72419 / 0.26 ( 6) link_NAG-ASN : bond 0.07018 / 4.05 ( 5) link_NAG-ASN : angle 3.89333 / 2.53 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 0.357 Fit side-chains REVERT: A 1556 PHE cc_start: 0.8519 (t80) cc_final: 0.7954 (t80) outliers start: 5 outliers final: 0 residues processed: 116 average time/residue: 0.4619 time to fit residues: 58.2505 Evaluate side-chains 78 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.0670 chunk 106 optimal weight: 0.9990 overall best weight: 0.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 ASN A 390 ASN A1140 GLN ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1631 HIS A Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.111011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.076035 restraints weight = 30294.264| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.11 r_work: 0.2954 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9980 Z= 0.152 Angle : 0.750 10.006 13492 Z= 0.370 Chirality : 0.045 0.340 1521 Planarity : 0.004 0.035 1541 Dihedral : 19.700 168.030 1710 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.82 % Allowed : 12.26 % Favored : 86.92 % 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: 0.73 (0.26), residues: 1093 helix: 1.40 (0.19), residues: 751 sheet: -3.06 (0.87), residues: 22 loop : -1.45 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 756 TYR 0.031 0.002 TYR A1717 PHE 0.032 0.001 PHE A 194 TRP 0.017 0.001 TRP A1663 HIS 0.003 0.001 HIS A 837 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 9968) covalent geometry : angle 0.74187 / 0.37 (13461) SS BOND : bond 0.00323 / 0.18 ( 5) SS BOND : angle 2.15067 / 1.36 ( 10) hydrogen bonds : bond 0.05047 / 3.26 ( 579) hydrogen bonds : angle 4.83550 / 3.40 ( 1707) link_BETA1-4 : bond 0.00350 / 0.18 ( 2) link_BETA1-4 : angle 2.10055 / 0.89 ( 6) link_NAG-ASN : bond 0.00503 / 0.25 ( 5) link_NAG-ASN : angle 2.56520 / 1.50 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 1435 MET cc_start: 0.8193 (mtt) cc_final: 0.7871 (mtm) REVERT: A 1556 PHE cc_start: 0.8647 (t80) cc_final: 0.7958 (t80) outliers start: 8 outliers final: 3 residues processed: 89 average time/residue: 0.4282 time to fit residues: 41.5671 Evaluate side-chains 78 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 TYR Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 1140 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 2 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 100 optimal weight: 0.1980 chunk 59 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 78 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 ASN A 878 ASN ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1422 ASN A1439 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.111505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.076614 restraints weight = 32094.506| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.06 r_work: 0.2986 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9980 Z= 0.136 Angle : 0.672 10.183 13492 Z= 0.334 Chirality : 0.043 0.394 1521 Planarity : 0.004 0.030 1541 Dihedral : 18.144 170.600 1710 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.13 % Allowed : 13.59 % Favored : 85.27 % 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: 0.91 (0.26), residues: 1093 helix: 1.53 (0.19), residues: 749 sheet: -2.96 (0.89), residues: 22 loop : -1.36 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 756 TYR 0.020 0.002 TYR A 400 PHE 0.025 0.001 PHE A 194 TRP 0.013 0.001 TRP A1663 HIS 0.002 0.001 HIS A 837 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 9968) covalent geometry : angle 0.66335 / 0.33 (13461) SS BOND : bond 0.00301 / 0.16 ( 5) SS BOND : angle 1.63592 / 1.02 ( 10) hydrogen bonds : bond 0.04500 / 2.88 ( 579) hydrogen bonds : angle 4.55499 / 3.19 ( 1707) link_BETA1-4 : bond 0.00403 / 0.20 ( 2) link_BETA1-4 : angle 2.03137 / 0.98 ( 6) link_NAG-ASN : bond 0.00577 / 0.28 ( 5) link_NAG-ASN : angle 2.82715 / 1.64 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.346 Fit side-chains REVERT: A 1435 MET cc_start: 0.8253 (mtt) cc_final: 0.7892 (mtm) REVERT: A 1556 PHE cc_start: 0.8623 (t80) cc_final: 0.7944 (t80) REVERT: A 1713 MET cc_start: 0.9097 (ptt) cc_final: 0.8802 (ttp) outliers start: 11 outliers final: 3 residues processed: 85 average time/residue: 0.3970 time to fit residues: 37.1316 Evaluate side-chains 75 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1641 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 77 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.111533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.075790 restraints weight = 35193.929| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.32 r_work: 0.2939 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9980 Z= 0.126 Angle : 0.633 10.275 13492 Z= 0.312 Chirality : 0.042 0.366 1521 Planarity : 0.004 0.029 1541 Dihedral : 16.707 174.068 1710 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.44 % Allowed : 14.73 % Favored : 83.83 % 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: 1.09 (0.26), residues: 1093 helix: 1.66 (0.19), residues: 750 sheet: -2.94 (0.93), residues: 22 loop : -1.27 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 756 TYR 0.021 0.002 TYR A 400 PHE 0.022 0.001 PHE A 194 TRP 0.012 0.001 TRP A1663 HIS 0.001 0.001 HIS A 837 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 9968) covalent geometry : angle 0.62529 / 0.31 (13461) SS BOND : bond 0.00329 / 0.18 ( 5) SS BOND : angle 1.41269 / 0.87 ( 10) hydrogen bonds : bond 0.04080 / 2.59 ( 579) hydrogen bonds : angle 4.34768 / 3.04 ( 1707) link_BETA1-4 : bond 0.00306 / 0.16 ( 2) link_BETA1-4 : angle 1.90956 / 0.87 ( 6) link_NAG-ASN : bond 0.00572 / 0.28 ( 5) link_NAG-ASN : angle 2.67641 / 1.55 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.228 Fit side-chains REVERT: A 1435 MET cc_start: 0.8191 (mtt) cc_final: 0.7968 (mtm) REVERT: A 1556 PHE cc_start: 0.8638 (t80) cc_final: 0.7956 (t80) REVERT: A 1713 MET cc_start: 0.9124 (ptt) cc_final: 0.8912 (ttp) outliers start: 14 outliers final: 4 residues processed: 90 average time/residue: 0.4395 time to fit residues: 43.3058 Evaluate side-chains 80 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1422 ASN Chi-restraints excluded: chain A residue 1524 VAL Chi-restraints excluded: chain A residue 1641 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1444 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.108574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.071748 restraints weight = 41524.675| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.60 r_work: 0.2857 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 9980 Z= 0.178 Angle : 0.653 9.831 13492 Z= 0.325 Chirality : 0.044 0.415 1521 Planarity : 0.004 0.030 1541 Dihedral : 16.276 176.747 1710 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.24 % Allowed : 16.48 % Favored : 82.29 % 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: 0.98 (0.26), residues: 1093 helix: 1.50 (0.18), residues: 763 sheet: -2.97 (0.94), residues: 22 loop : -1.20 (0.38), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 756 TYR 0.025 0.002 TYR A 400 PHE 0.018 0.001 PHE A 194 TRP 0.013 0.001 TRP A1369 HIS 0.002 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 9968) covalent geometry : angle 0.64448 / 0.32 (13461) SS BOND : bond 0.00577 / 0.29 ( 5) SS BOND : angle 1.68297 / 1.03 ( 10) hydrogen bonds : bond 0.04374 / 2.80 ( 579) hydrogen bonds : angle 4.42902 / 3.11 ( 1707) link_BETA1-4 : bond 0.00031 / 0.02 ( 2) link_BETA1-4 : angle 1.97943 / 0.92 ( 6) link_NAG-ASN : bond 0.00533 / 0.28 ( 5) link_NAG-ASN : angle 2.81523 / 1.63 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.380 Fit side-chains REVERT: A 1435 MET cc_start: 0.8206 (mtt) cc_final: 0.7915 (mtm) REVERT: A 1556 PHE cc_start: 0.8652 (t80) cc_final: 0.7970 (t80) REVERT: A 1564 GLN cc_start: 0.7425 (mm110) cc_final: 0.6973 (mp10) REVERT: A 1713 MET cc_start: 0.9205 (ptt) cc_final: 0.8987 (ttp) outliers start: 12 outliers final: 5 residues processed: 81 average time/residue: 0.4511 time to fit residues: 40.1844 Evaluate side-chains 77 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1290 ILE Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1422 ASN Chi-restraints excluded: chain A residue 1524 VAL Chi-restraints excluded: chain A residue 1641 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 30 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 0.0000 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 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 = 0.3739 r_free = 0.3739 target = 0.107646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.071776 restraints weight = 35268.454| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.18 r_work: 0.2857 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9980 Z= 0.203 Angle : 0.673 10.785 13492 Z= 0.330 Chirality : 0.045 0.395 1521 Planarity : 0.004 0.031 1541 Dihedral : 16.049 179.115 1710 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.65 % Allowed : 16.27 % Favored : 82.08 % 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: 0.92 (0.26), residues: 1093 helix: 1.45 (0.18), residues: 762 sheet: -2.96 (0.98), residues: 22 loop : -1.19 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 814 TYR 0.025 0.002 TYR A 400 PHE 0.017 0.002 PHE A 386 TRP 0.016 0.001 TRP A1369 HIS 0.002 0.001 HIS A 687 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 ( 9968) covalent geometry : angle 0.66388 / 0.33 (13461) SS BOND : bond 0.00706 / 0.35 ( 5) SS BOND : angle 1.74856 / 1.08 ( 10) hydrogen bonds : bond 0.04450 / 2.85 ( 579) hydrogen bonds : angle 4.45455 / 3.12 ( 1707) link_BETA1-4 : bond 0.00133 / 0.06 ( 2) link_BETA1-4 : angle 2.00778 / 0.97 ( 6) link_NAG-ASN : bond 0.00486 / 0.26 ( 5) link_NAG-ASN : angle 2.82426 / 1.65 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 654 LEU cc_start: 0.7277 (mm) cc_final: 0.7057 (mm) REVERT: A 824 HIS cc_start: 0.8358 (OUTLIER) cc_final: 0.8088 (t-90) REVERT: A 1435 MET cc_start: 0.8273 (mtt) cc_final: 0.7954 (mtm) REVERT: A 1556 PHE cc_start: 0.8667 (t80) cc_final: 0.7984 (t80) REVERT: A 1564 GLN cc_start: 0.7363 (mm110) cc_final: 0.6919 (mp10) REVERT: A 1713 MET cc_start: 0.9146 (ptt) cc_final: 0.8829 (ttp) outliers start: 16 outliers final: 5 residues processed: 81 average time/residue: 0.4269 time to fit residues: 38.0001 Evaluate side-chains 77 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 824 HIS Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1422 ASN Chi-restraints excluded: chain A residue 1524 VAL Chi-restraints excluded: chain A residue 1641 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 69 optimal weight: 0.0270 chunk 43 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 ASN A 390 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.110259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.074572 restraints weight = 35474.222| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.22 r_work: 0.2920 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9980 Z= 0.118 Angle : 0.615 11.099 13492 Z= 0.301 Chirality : 0.042 0.383 1521 Planarity : 0.004 0.032 1541 Dihedral : 15.254 176.041 1710 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.03 % Allowed : 17.20 % Favored : 81.77 % 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: 1.11 (0.26), residues: 1093 helix: 1.64 (0.19), residues: 760 sheet: -3.06 (0.96), residues: 22 loop : -1.23 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 215 TYR 0.021 0.001 TYR A 400 PHE 0.025 0.001 PHE A 386 TRP 0.010 0.001 TRP A1343 HIS 0.001 0.000 HIS A 837 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 9968) covalent geometry : angle 0.60684 / 0.30 (13461) SS BOND : bond 0.00260 / 0.13 ( 5) SS BOND : angle 1.15428 / 0.70 ( 10) hydrogen bonds : bond 0.03907 / 2.49 ( 579) hydrogen bonds : angle 4.28806 / 3.00 ( 1707) link_BETA1-4 : bond 0.00446 / 0.23 ( 2) link_BETA1-4 : angle 2.11515 / 0.96 ( 6) link_NAG-ASN : bond 0.00454 / 0.22 ( 5) link_NAG-ASN : angle 2.64224 / 1.51 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.344 Fit side-chains REVERT: A 1435 MET cc_start: 0.8247 (mtt) cc_final: 0.7926 (mtm) REVERT: A 1556 PHE cc_start: 0.8643 (t80) cc_final: 0.7941 (t80) REVERT: A 1564 GLN cc_start: 0.7368 (mm110) cc_final: 0.6903 (mp10) outliers start: 10 outliers final: 3 residues processed: 75 average time/residue: 0.4231 time to fit residues: 34.8361 Evaluate side-chains 73 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 1422 ASN Chi-restraints excluded: chain A residue 1641 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 5.9990 chunk 14 optimal weight: 0.0670 chunk 91 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.110212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.072074 restraints weight = 43509.067| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.65 r_work: 0.2888 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9980 Z= 0.126 Angle : 0.621 11.378 13492 Z= 0.303 Chirality : 0.042 0.354 1521 Planarity : 0.003 0.031 1541 Dihedral : 14.938 174.585 1710 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.82 % Allowed : 17.71 % Favored : 81.46 % 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: 1.11 (0.26), residues: 1093 helix: 1.64 (0.19), residues: 760 sheet: -3.08 (0.98), residues: 22 loop : -1.22 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 221 TYR 0.033 0.002 TYR A1717 PHE 0.028 0.001 PHE A 386 TRP 0.008 0.001 TRP A1663 HIS 0.001 0.001 HIS A 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 9968) covalent geometry : angle 0.61377 / 0.30 (13461) SS BOND : bond 0.00366 / 0.18 ( 5) SS BOND : angle 1.17093 / 0.71 ( 10) hydrogen bonds : bond 0.03920 / 2.50 ( 579) hydrogen bonds : angle 4.30138 / 3.01 ( 1707) link_BETA1-4 : bond 0.00330 / 0.17 ( 2) link_BETA1-4 : angle 1.95083 / 0.91 ( 6) link_NAG-ASN : bond 0.00388 / 0.19 ( 5) link_NAG-ASN : angle 2.48207 / 1.43 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.308 Fit side-chains REVERT: A 1435 MET cc_start: 0.8272 (mtt) cc_final: 0.7965 (mtm) REVERT: A 1556 PHE cc_start: 0.8658 (t80) cc_final: 0.7957 (t80) REVERT: A 1564 GLN cc_start: 0.7378 (mm110) cc_final: 0.6932 (mp10) REVERT: A 1717 TYR cc_start: 0.8687 (m-80) cc_final: 0.8401 (m-80) outliers start: 8 outliers final: 4 residues processed: 73 average time/residue: 0.4552 time to fit residues: 36.4138 Evaluate side-chains 74 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 1422 ASN Chi-restraints excluded: chain A residue 1641 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 364 GLN A 878 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.110485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.074566 restraints weight = 36454.566| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.34 r_work: 0.2917 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9980 Z= 0.120 Angle : 0.602 11.056 13492 Z= 0.296 Chirality : 0.042 0.347 1521 Planarity : 0.003 0.031 1541 Dihedral : 14.353 171.442 1710 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.93 % Allowed : 17.61 % Favored : 81.46 % 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: 1.19 (0.26), residues: 1093 helix: 1.73 (0.19), residues: 749 sheet: -3.09 (0.98), residues: 22 loop : -1.19 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1460 TYR 0.026 0.001 TYR A1717 PHE 0.026 0.001 PHE A 386 TRP 0.018 0.001 TRP A 850 HIS 0.001 0.000 HIS A 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 9968) covalent geometry : angle 0.59538 / 0.29 (13461) SS BOND : bond 0.00320 / 0.16 ( 5) SS BOND : angle 1.12497 / 0.68 ( 10) hydrogen bonds : bond 0.03818 / 2.43 ( 579) hydrogen bonds : angle 4.27829 / 2.99 ( 1707) link_BETA1-4 : bond 0.00371 / 0.19 ( 2) link_BETA1-4 : angle 1.89117 / 0.88 ( 6) link_NAG-ASN : bond 0.00385 / 0.19 ( 5) link_NAG-ASN : angle 2.43305 / 1.40 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.380 Fit side-chains REVERT: A 1435 MET cc_start: 0.8253 (mtt) cc_final: 0.7918 (mtm) REVERT: A 1556 PHE cc_start: 0.8662 (t80) cc_final: 0.7916 (t80) REVERT: A 1564 GLN cc_start: 0.7254 (mm110) cc_final: 0.6873 (mp10) outliers start: 9 outliers final: 3 residues processed: 75 average time/residue: 0.4602 time to fit residues: 38.0860 Evaluate side-chains 73 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1422 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 23 optimal weight: 0.8980 chunk 7 optimal weight: 0.0170 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 0.0770 chunk 4 optimal weight: 40.0000 chunk 94 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 overall best weight: 0.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.112102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.074108 restraints weight = 44403.336| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.70 r_work: 0.2938 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9980 Z= 0.112 Angle : 0.606 11.709 13492 Z= 0.296 Chirality : 0.041 0.333 1521 Planarity : 0.003 0.032 1541 Dihedral : 13.709 168.752 1710 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.31 % Allowed : 18.54 % Favored : 81.15 % 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: 1.26 (0.26), residues: 1093 helix: 1.79 (0.19), residues: 749 sheet: -3.09 (0.98), residues: 22 loop : -1.18 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 756 TYR 0.036 0.001 TYR A1717 PHE 0.026 0.001 PHE A 386 TRP 0.014 0.001 TRP A1369 HIS 0.001 0.000 HIS A 837 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 9968) covalent geometry : angle 0.60004 / 0.29 (13461) SS BOND : bond 0.00169 / 0.09 ( 5) SS BOND : angle 0.98318 / 0.59 ( 10) hydrogen bonds : bond 0.03642 / 2.32 ( 579) hydrogen bonds : angle 4.23194 / 2.95 ( 1707) link_BETA1-4 : bond 0.00359 / 0.18 ( 2) link_BETA1-4 : angle 1.89013 / 0.84 ( 6) link_NAG-ASN : bond 0.00446 / 0.22 ( 5) link_NAG-ASN : angle 2.32151 / 1.33 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.347 Fit side-chains REVERT: A 386 PHE cc_start: 0.8263 (t80) cc_final: 0.8055 (t80) REVERT: A 1201 MET cc_start: 0.8836 (ttm) cc_final: 0.8492 (ttm) REVERT: A 1435 MET cc_start: 0.8250 (mtt) cc_final: 0.7925 (mtm) REVERT: A 1556 PHE cc_start: 0.8667 (t80) cc_final: 0.7928 (t80) REVERT: A 1564 GLN cc_start: 0.7134 (mm110) cc_final: 0.6776 (mp10) outliers start: 3 outliers final: 1 residues processed: 75 average time/residue: 0.4424 time to fit residues: 36.4733 Evaluate side-chains 68 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1422 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 52 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3796 r_free = 0.3796 target = 0.111060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.073021 restraints weight = 43816.759| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.67 r_work: 0.2908 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9980 Z= 0.129 Angle : 0.610 11.203 13492 Z= 0.301 Chirality : 0.041 0.328 1521 Planarity : 0.003 0.031 1541 Dihedral : 13.460 166.793 1710 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.31 % Allowed : 18.74 % Favored : 80.95 % 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: 1.20 (0.26), residues: 1093 helix: 1.75 (0.18), residues: 750 sheet: -3.06 (1.00), residues: 22 loop : -1.20 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1460 TYR 0.029 0.002 TYR A1717 PHE 0.031 0.001 PHE A 707 TRP 0.008 0.001 TRP A 850 HIS 0.001 0.000 HIS A 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 9968) covalent geometry : angle 0.60392 / 0.30 (13461) SS BOND : bond 0.00369 / 0.19 ( 5) SS BOND : angle 1.11372 / 0.67 ( 10) hydrogen bonds : bond 0.03791 / 2.42 ( 579) hydrogen bonds : angle 4.28083 / 2.99 ( 1707) link_BETA1-4 : bond 0.00377 / 0.19 ( 2) link_BETA1-4 : angle 1.73856 / 0.83 ( 6) link_NAG-ASN : bond 0.00375 / 0.19 ( 5) link_NAG-ASN : angle 2.38803 / 1.38 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2991.25 seconds wall clock time: 51 minutes 50.44 seconds (3110.44 seconds total)