Starting phenix.real_space_refine on Fri Jul 3 02:00:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iti_60867/07_2026/9iti_60867.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iti_60867/07_2026/9iti_60867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iti_60867/07_2026/9iti_60867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iti_60867/07_2026/9iti_60867.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iti_60867/07_2026/9iti_60867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iti_60867/07_2026/9iti_60867.map" } resolution = 2.92 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= 0.082 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 18 5.49 5 S 77 5.16 5 Na 1 4.78 5 C 7419 2.51 5 N 1638 2.21 5 O 1933 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 129 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: 11086 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10250 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1268, 10236 Classifications: {'peptide': 1268} Link IDs: {'PTRANS': 41, 'TRANS': 1226} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 1268, 10236 Classifications: {'peptide': 1268} Link IDs: {'PTRANS': 41, 'TRANS': 1226} Chain breaks: 6 bond proxies already assigned to first conformer: 10467 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 779 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'1PW': 1, '9Z9': 1, 'LPE': 10, 'NAG': 2, 'PCW': 5, 'Y01': 4} Classifications: {'peptide': 2, 'undetermined': 23} Link IDs: {None: 23} Chain breaks: 1 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'P5S:plan-2': 1, '1PW:plan-1': 1, 'P5S:plan-1': 1, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 16 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP A 190 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A 190 " occ=0.50 Time building chain proxies: 4.12, per 1000 atoms: 0.37 Number of scatterers: 11086 At special positions: 0 Unit cell: (107.594, 129.552, 127.356, 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) S 77 16.00 P 18 15.00 Na 1 11.00 O 1933 8.00 N 1638 7.00 C 7419 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.03 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.03 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.02 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1729 " distance=2.02 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 283 " " NAG A2002 " - " ASN A1375 " " NAG B 1 " - " ASN A1352 " " NAG C 1 " - " ASN A1366 " Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 606.8 milliseconds 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2402 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 3 sheets defined 77.9% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 16 through 34 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.917A pdb=" N VAL A 71 " --> pdb=" O PRO A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 125 through 144 removed outlier: 3.829A pdb=" N SER A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 175 removed outlier: 4.340A pdb=" N VAL A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 185 Processing helix chain 'A' and resid 186 through 205 removed outlier: 3.955A pdb=" N ATRP A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.811A pdb=" N PHE A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.858A pdb=" N LYS A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 268 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.903A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 Processing helix chain 'A' and resid 389 through 425 removed outlier: 3.729A pdb=" N LEU A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 741 Processing helix chain 'A' and resid 742 through 762 removed outlier: 3.669A pdb=" N ASP A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 748 " --> pdb=" O PRO A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 798 removed outlier: 3.760A pdb=" N MET A 798 " --> pdb=" O LYS A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 804 removed outlier: 3.751A pdb=" N PHE A 804 " --> pdb=" O PRO A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 825 removed outlier: 4.222A pdb=" N LEU A 825 " --> pdb=" O VAL A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 847 removed outlier: 3.707A pdb=" N PHE A 837 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG A 838 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 864 removed outlier: 3.760A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 895 removed outlier: 3.543A pdb=" N THR A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 899 Processing helix chain 'A' and resid 912 through 926 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.837A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 974 removed outlier: 3.763A pdb=" N CYS A 944 " --> pdb=" O GLY A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1014 Processing helix chain 'A' and resid 1176 through 1191 Processing helix chain 'A' and resid 1191 through 1209 Processing helix chain 'A' and resid 1210 through 1212 No H-bonds generated for 'chain 'A' and resid 1210 through 1212' Processing helix chain 'A' and resid 1219 through 1249 removed outlier: 3.806A pdb=" N ILE A1224 " --> pdb=" O LYS A1220 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A1225 " --> pdb=" O THR A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1255 Processing helix chain 'A' and resid 1256 through 1279 Processing helix chain 'A' and resid 1283 through 1292 removed outlier: 3.871A pdb=" N THR A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A1292 " --> pdb=" O SER A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1303 Proline residue: A1297 - end of helix removed outlier: 3.867A pdb=" N SER A1302 " --> pdb=" O ARG A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1317 Processing helix chain 'A' and resid 1317 through 1344 Processing helix chain 'A' and resid 1366 through 1377 Processing helix chain 'A' and resid 1391 through 1404 Processing helix chain 'A' and resid 1407 through 1417 removed outlier: 3.735A pdb=" N ILE A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1432 No H-bonds generated for 'chain 'A' and resid 1430 through 1432' Processing helix chain 'A' and resid 1433 through 1445 removed outlier: 3.849A pdb=" N PHE A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1467 Processing helix chain 'A' and resid 1475 through 1490 Processing helix chain 'A' and resid 1502 through 1513 Processing helix chain 'A' and resid 1514 through 1534 removed outlier: 3.600A pdb=" N ASP A1518 " --> pdb=" O ASN A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1570 Processing helix chain 'A' and resid 1571 through 1575 Processing helix chain 'A' and resid 1576 through 1600 removed outlier: 3.968A pdb=" N ILE A1580 " --> pdb=" O VAL A1576 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A1581 " --> pdb=" O GLY A1577 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A1597 " --> pdb=" O MET A1593 " (cutoff:3.500A) Processing helix chain 'A' and resid 1605 through 1613 Processing helix chain 'A' and resid 1616 through 1621 removed outlier: 4.210A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A1621 " --> pdb=" O ILE A1617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1616 through 1621' Processing helix chain 'A' and resid 1622 through 1626 removed outlier: 3.573A pdb=" N GLY A1626 " --> pdb=" O LEU A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1667 removed outlier: 3.509A pdb=" N THR A1632 " --> pdb=" O LYS A1628 " (cutoff:3.500A) Proline residue: A1642 - end of helix removed outlier: 3.894A pdb=" N ALA A1667 " --> pdb=" O MET A1663 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 3.503A pdb=" N CYS A1690 " --> pdb=" O ASN A1686 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1708 Proline residue: A1706 - end of helix Processing helix chain 'A' and resid 1731 through 1765 Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 91 Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 277 Processing sheet with id=AA3, first strand: chain 'A' and resid 1357 through 1358 708 hydrogen bonds defined for protein. 2031 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: 1.81 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1612 1.29 - 1.43: 2939 1.43 - 1.56: 6597 1.56 - 1.69: 60 1.69 - 1.82: 127 Bond restraints: 11335 Sorted by residual: bond pdb=" CA GLU A1212 " pdb=" C GLU A1212 " ideal model delta sigma weight residual 1.526 1.438 0.088 1.21e-02 6.83e+03 5.31e+01 bond pdb=" C11 PCW A2009 " pdb=" O3 PCW A2009 " ideal model delta sigma weight residual 1.326 1.460 -0.134 2.00e-02 2.50e+03 4.49e+01 bond pdb=" C11 PCW A2020 " pdb=" O3 PCW A2020 " ideal model delta sigma weight residual 1.326 1.458 -0.132 2.00e-02 2.50e+03 4.34e+01 bond pdb=" C11 PCW A2021 " pdb=" O3 PCW A2021 " ideal model delta sigma weight residual 1.326 1.458 -0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" C31 PCW A2014 " pdb=" O2 PCW A2014 " ideal model delta sigma weight residual 1.333 1.463 -0.130 2.00e-02 2.50e+03 4.20e+01 ... (remaining 11330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 14559 2.72 - 5.45: 557 5.45 - 8.17: 141 8.17 - 10.90: 36 10.90 - 13.62: 7 Bond angle restraints: 15300 Sorted by residual: angle pdb=" N PHE A 344 " pdb=" CA PHE A 344 " pdb=" C PHE A 344 " ideal model delta sigma weight residual 111.30 100.74 10.56 1.43e+00 4.89e-01 5.46e+01 angle pdb=" C TYR A1481 " pdb=" CA TYR A1481 " pdb=" CB TYR A1481 " ideal model delta sigma weight residual 110.88 101.73 9.15 1.57e+00 4.06e-01 3.39e+01 angle pdb=" N SER A1568 " pdb=" CA SER A1568 " pdb=" C SER A1568 " ideal model delta sigma weight residual 111.36 117.34 -5.98 1.09e+00 8.42e-01 3.01e+01 angle pdb=" N TYR A 341 " pdb=" CA TYR A 341 " pdb=" C TYR A 341 " ideal model delta sigma weight residual 113.17 119.88 -6.71 1.26e+00 6.30e-01 2.84e+01 angle pdb=" C LEU A 304 " pdb=" CA LEU A 304 " pdb=" CB LEU A 304 " ideal model delta sigma weight residual 110.19 102.15 8.04 1.62e+00 3.81e-01 2.46e+01 ... (remaining 15295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.76: 6606 28.76 - 57.52: 516 57.52 - 86.28: 62 86.28 - 115.05: 22 115.05 - 143.81: 23 Dihedral angle restraints: 7229 sinusoidal: 3513 harmonic: 3716 Sorted by residual: dihedral pdb=" CA ILE A1351 " pdb=" C ILE A1351 " pdb=" N ASN A1352 " pdb=" CA ASN A1352 " ideal model delta harmonic sigma weight residual 180.00 150.12 29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" C ASN A 282 " pdb=" N ASN A 282 " pdb=" CA ASN A 282 " pdb=" CB ASN A 282 " ideal model delta harmonic sigma weight residual -122.60 -136.74 14.14 0 2.50e+00 1.60e-01 3.20e+01 dihedral pdb=" N ASN A 282 " pdb=" C ASN A 282 " pdb=" CA ASN A 282 " pdb=" CB ASN A 282 " ideal model delta harmonic sigma weight residual 122.80 136.67 -13.87 0 2.50e+00 1.60e-01 3.08e+01 ... (remaining 7226 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1622 0.128 - 0.257: 72 0.257 - 0.385: 22 0.385 - 0.513: 3 0.513 - 0.642: 7 Chirality restraints: 1726 Sorted by residual: chirality pdb=" CA TYR A 341 " pdb=" N TYR A 341 " pdb=" C TYR A 341 " pdb=" CB TYR A 341 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C1 NAG A2002 " pdb=" ND2 ASN A1375 " pdb=" C2 NAG A2002 " pdb=" O5 NAG A2002 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.02e+00 chirality pdb=" CA ASN A 282 " pdb=" N ASN A 282 " pdb=" C ASN A 282 " pdb=" CB ASN A 282 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.23e+00 ... (remaining 1723 not shown) Planarity restraints: 1778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAH 1PW A2007 " 0.415 2.00e-02 2.50e+03 2.54e-01 6.46e+02 pdb=" CAI 1PW A2007 " -0.221 2.00e-02 2.50e+03 pdb=" CAK 1PW A2007 " -0.193 2.00e-02 2.50e+03 pdb=" CAZ 1PW A2007 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1408 " 0.020 2.00e-02 2.50e+03 2.71e-02 1.84e+01 pdb=" CG TRP A1408 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP A1408 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP A1408 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A1408 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A1408 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A1408 " 0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1408 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1408 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A1408 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 342 " -0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C THR A 342 " 0.069 2.00e-02 2.50e+03 pdb=" O THR A 342 " -0.027 2.00e-02 2.50e+03 pdb=" N SER A 343 " -0.023 2.00e-02 2.50e+03 ... (remaining 1775 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1505 2.74 - 3.28: 11297 3.28 - 3.82: 17828 3.82 - 4.36: 21684 4.36 - 4.90: 36536 Nonbonded interactions: 88850 Sorted by model distance: nonbonded pdb=" O GLU A 29 " pdb=" OG SER A 32 " model vdw 2.205 3.040 nonbonded pdb=" OD1 ASN A 92 " pdb=" OG1 THR A 96 " model vdw 2.215 3.040 nonbonded pdb=" C31 LPE A2015 " pdb=" C3N LPE A2015 " model vdw 2.288 3.088 nonbonded pdb=" C4 PCW A2012 " pdb=" C8 PCW A2012 " model vdw 2.303 3.088 nonbonded pdb=" O1 LPE A2010 " pdb=" O2H LPE A2010 " model vdw 2.312 2.432 ... (remaining 88845 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 12.850 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 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:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 : 0.011 0.134 11347 Z= 0.608 Angle : 1.331 13.620 15330 Z= 0.630 Chirality : 0.077 0.642 1726 Planarity : 0.008 0.254 1774 Dihedral : 21.382 143.806 4809 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.88 % Allowed : 1.32 % Favored : 97.79 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.23), residues: 1257 helix: 0.24 (0.17), residues: 881 sheet: -2.17 (0.83), residues: 27 loop : -0.92 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG A 117 TYR 0.045 0.003 TYR A 362 PHE 0.059 0.003 PHE A 344 TRP 0.070 0.003 TRP A1408 HIS 0.006 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.01119 / 0.61 (11335) covalent geometry : angle 1.31600 / 0.63 (15300) SS BOND : bond 0.00560 / 0.39 ( 6) SS BOND : angle 3.26863 / 2.23 ( 12) hydrogen bonds : bond 0.13937 / 8.75 ( 708) hydrogen bonds : angle 6.18370 / 4.37 ( 2031) link_BETA1-4 : bond 0.00456 / 0.28 ( 2) link_BETA1-4 : angle 3.96216 / 2.08 ( 6) link_NAG-ASN : bond 0.01286 / 0.88 ( 4) link_NAG-ASN : angle 6.03529 / 3.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 202 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 910 MET cc_start: 0.8848 (mtp) cc_final: 0.8599 (mtm) REVERT: A 1221 THR cc_start: 0.8158 (p) cc_final: 0.7905 (t) REVERT: A 1541 GLN cc_start: 0.7623 (mp10) cc_final: 0.7278 (mp10) outliers start: 9 outliers final: 4 residues processed: 208 average time/residue: 0.3944 time to fit residues: 90.3282 Evaluate side-chains 166 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 162 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 1238 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.0570 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 HIS A 139 ASN A 147 ASN A 154 ASN ** A 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN A 336 ASN A 395 ASN A 757 ASN ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1312 ASN A1363 GLN A1462 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.184383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.142733 restraints weight = 26258.511| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 5.39 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 11347 Z= 0.151 Angle : 0.764 17.114 15330 Z= 0.377 Chirality : 0.046 0.307 1726 Planarity : 0.005 0.050 1774 Dihedral : 19.007 160.544 2402 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.21 % Allowed : 12.62 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.32 (0.23), residues: 1257 helix: 0.78 (0.16), residues: 890 sheet: -2.25 (0.73), residues: 39 loop : -0.81 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 117 TYR 0.020 0.002 TYR A 362 PHE 0.045 0.002 PHE A1233 TRP 0.036 0.002 TRP A1408 HIS 0.002 0.001 HIS A1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (11335) covalent geometry : angle 0.75218 / 0.37 (15300) SS BOND : bond 0.00566 / 0.32 ( 6) SS BOND : angle 2.40607 / 1.63 ( 12) hydrogen bonds : bond 0.04906 / 3.16 ( 708) hydrogen bonds : angle 4.89246 / 3.48 ( 2031) link_BETA1-4 : bond 0.00479 / 0.30 ( 2) link_BETA1-4 : angle 2.85546 / 1.32 ( 6) link_NAG-ASN : bond 0.01049 / 0.79 ( 4) link_NAG-ASN : angle 3.85640 / 2.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.404 Fit side-chains REVERT: A 324 CYS cc_start: 0.6145 (m) cc_final: 0.5927 (m) REVERT: A 407 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7771 (pp20) REVERT: A 1221 THR cc_start: 0.8210 (p) cc_final: 0.7981 (t) REVERT: A 1252 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.8037 (t) REVERT: A 1548 TYR cc_start: 0.8471 (t80) cc_final: 0.7845 (t80) outliers start: 24 outliers final: 5 residues processed: 187 average time/residue: 0.4261 time to fit residues: 87.9729 Evaluate side-chains 168 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 161 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1252 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 89 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN A 147 ASN ** A 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 ASN A 757 ASN ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1363 GLN A1462 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.180322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.120744 restraints weight = 25123.742| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.98 r_work: 0.3247 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11347 Z= 0.169 Angle : 0.716 10.929 15330 Z= 0.359 Chirality : 0.045 0.304 1726 Planarity : 0.005 0.049 1774 Dihedral : 17.428 148.208 2396 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.12 % Allowed : 16.33 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.23), residues: 1257 helix: 1.00 (0.16), residues: 895 sheet: -1.91 (0.72), residues: 37 loop : -0.85 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 26 TYR 0.024 0.002 TYR A 362 PHE 0.028 0.002 PHE A1233 TRP 0.032 0.002 TRP A1179 HIS 0.003 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (11335) covalent geometry : angle 0.70436 / 0.36 (15300) SS BOND : bond 0.00325 / 0.25 ( 6) SS BOND : angle 2.19632 / 1.51 ( 12) hydrogen bonds : bond 0.04754 / 3.06 ( 708) hydrogen bonds : angle 4.76978 / 3.39 ( 2031) link_BETA1-4 : bond 0.00651 / 0.39 ( 2) link_BETA1-4 : angle 3.03673 / 1.47 ( 6) link_NAG-ASN : bond 0.00968 / 0.68 ( 4) link_NAG-ASN : angle 3.58387 / 2.25 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.406 Fit side-chains REVERT: A 407 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7864 (pp20) REVERT: A 791 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.6683 (tpt) REVERT: A 903 CYS cc_start: 0.6937 (m) cc_final: 0.6701 (m) REVERT: A 1221 THR cc_start: 0.8289 (p) cc_final: 0.8000 (t) REVERT: A 1252 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7994 (t) REVERT: A 1541 GLN cc_start: 0.7631 (mp10) cc_final: 0.7404 (mm-40) REVERT: A 1548 TYR cc_start: 0.8963 (t80) cc_final: 0.8414 (t80) REVERT: A 1583 PHE cc_start: 0.8764 (t80) cc_final: 0.8561 (t80) REVERT: A 1613 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7843 (ttt90) outliers start: 23 outliers final: 7 residues processed: 177 average time/residue: 0.4292 time to fit residues: 83.6079 Evaluate side-chains 164 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1252 THR Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1613 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 0.0670 chunk 118 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 overall best weight: 0.6216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN ** A 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1363 GLN A1462 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.181968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124977 restraints weight = 27406.320| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 3.14 r_work: 0.3279 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 11347 Z= 0.140 Angle : 0.679 13.228 15330 Z= 0.342 Chirality : 0.044 0.306 1726 Planarity : 0.004 0.049 1774 Dihedral : 16.559 145.186 2396 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.77 % Allowed : 17.12 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.86 (0.23), residues: 1257 helix: 1.22 (0.17), residues: 890 sheet: -1.51 (0.75), residues: 37 loop : -0.83 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1293 TYR 0.019 0.002 TYR A 405 PHE 0.029 0.001 PHE A1233 TRP 0.023 0.002 TRP A1179 HIS 0.002 0.001 HIS A1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (11335) covalent geometry : angle 0.66661 / 0.34 (15300) SS BOND : bond 0.00399 / 0.29 ( 6) SS BOND : angle 2.51858 / 1.51 ( 12) hydrogen bonds : bond 0.04380 / 2.82 ( 708) hydrogen bonds : angle 4.61739 / 3.30 ( 2031) link_BETA1-4 : bond 0.00563 / 0.34 ( 2) link_BETA1-4 : angle 2.90191 / 1.36 ( 6) link_NAG-ASN : bond 0.00978 / 0.69 ( 4) link_NAG-ASN : angle 3.54509 / 2.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 407 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7841 (pp20) REVERT: A 791 MET cc_start: 0.7314 (tmm) cc_final: 0.6655 (tpt) REVERT: A 903 CYS cc_start: 0.6903 (m) cc_final: 0.6671 (m) REVERT: A 1221 THR cc_start: 0.8297 (p) cc_final: 0.8008 (t) REVERT: A 1548 TYR cc_start: 0.8970 (t80) cc_final: 0.8361 (t80) outliers start: 19 outliers final: 4 residues processed: 181 average time/residue: 0.4200 time to fit residues: 84.0646 Evaluate side-chains 167 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 162 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 748 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 115 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 HIS A 147 ASN A 273 HIS A 336 ASN ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1363 GLN A1462 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.181711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.136973 restraints weight = 17528.364| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.67 r_work: 0.3230 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 11347 Z= 0.147 Angle : 0.680 12.993 15330 Z= 0.339 Chirality : 0.043 0.300 1726 Planarity : 0.004 0.049 1774 Dihedral : 15.919 156.531 2396 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.29 % Allowed : 17.74 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1257 helix: 1.25 (0.17), residues: 894 sheet: -1.58 (0.70), residues: 39 loop : -0.80 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1293 TYR 0.020 0.002 TYR A 405 PHE 0.029 0.002 PHE A1583 TRP 0.018 0.002 TRP A1179 HIS 0.002 0.001 HIS A1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (11335) covalent geometry : angle 0.66768 / 0.34 (15300) SS BOND : bond 0.00285 / 0.23 ( 6) SS BOND : angle 1.81745 / 1.20 ( 12) hydrogen bonds : bond 0.04327 / 2.78 ( 708) hydrogen bonds : angle 4.57889 / 3.27 ( 2031) link_BETA1-4 : bond 0.00439 / 0.27 ( 2) link_BETA1-4 : angle 2.82612 / 1.35 ( 6) link_NAG-ASN : bond 0.00913 / 0.63 ( 4) link_NAG-ASN : angle 3.82515 / 2.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 297 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7735 (tp30) REVERT: A 791 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.6651 (tpt) REVERT: A 1221 THR cc_start: 0.8354 (p) cc_final: 0.8055 (t) REVERT: A 1252 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7981 (t) REVERT: A 1541 GLN cc_start: 0.7548 (mp10) cc_final: 0.7339 (mm-40) REVERT: A 1548 TYR cc_start: 0.8954 (t80) cc_final: 0.8397 (t80) REVERT: A 1609 PHE cc_start: 0.8107 (t80) cc_final: 0.7851 (t80) outliers start: 25 outliers final: 6 residues processed: 182 average time/residue: 0.3971 time to fit residues: 80.2630 Evaluate side-chains 167 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 1181 ILE Chi-restraints excluded: chain A residue 1252 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 45 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN A 147 ASN ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1363 GLN A1462 GLN A1761 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.182481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.140927 restraints weight = 23866.091| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 5.46 r_work: 0.3124 rms_B_bonded: 5.40 restraints_weight: 2.0000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11347 Z= 0.167 Angle : 0.699 13.801 15330 Z= 0.348 Chirality : 0.044 0.296 1726 Planarity : 0.004 0.050 1774 Dihedral : 15.607 168.037 2396 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.85 % Allowed : 18.98 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.86 (0.23), residues: 1257 helix: 1.22 (0.17), residues: 897 sheet: -1.35 (0.68), residues: 39 loop : -0.90 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1293 TYR 0.022 0.002 TYR A 405 PHE 0.027 0.002 PHE A1583 TRP 0.017 0.002 TRP A1245 HIS 0.006 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (11335) covalent geometry : angle 0.68650 / 0.34 (15300) SS BOND : bond 0.00321 / 0.25 ( 6) SS BOND : angle 1.81856 / 1.13 ( 12) hydrogen bonds : bond 0.04434 / 2.85 ( 708) hydrogen bonds : angle 4.58433 / 3.27 ( 2031) link_BETA1-4 : bond 0.00475 / 0.30 ( 2) link_BETA1-4 : angle 3.13641 / 1.44 ( 6) link_NAG-ASN : bond 0.00911 / 0.63 ( 4) link_NAG-ASN : angle 3.91618 / 2.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8450 (t0) cc_final: 0.7453 (p0) REVERT: A 297 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7590 (tp30) REVERT: A 791 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6592 (tpt) REVERT: A 798 MET cc_start: 0.7475 (ttm) cc_final: 0.7142 (tmm) REVERT: A 1252 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7982 (t) REVERT: A 1485 MET cc_start: 0.7186 (ttm) cc_final: 0.6955 (tmm) REVERT: A 1609 PHE cc_start: 0.8105 (t80) cc_final: 0.7867 (t80) outliers start: 20 outliers final: 8 residues processed: 180 average time/residue: 0.3684 time to fit residues: 73.8631 Evaluate side-chains 172 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 1181 ILE Chi-restraints excluded: chain A residue 1252 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 51 optimal weight: 0.0030 chunk 32 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 117 optimal weight: 0.0050 overall best weight: 0.4606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 HIS A 92 ASN ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN A1761 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.183269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.142691 restraints weight = 29388.307| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 6.18 r_work: 0.3150 rms_B_bonded: 5.66 restraints_weight: 2.0000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11347 Z= 0.131 Angle : 0.676 14.555 15330 Z= 0.334 Chirality : 0.043 0.299 1726 Planarity : 0.004 0.049 1774 Dihedral : 14.947 179.122 2396 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.77 % Allowed : 20.39 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.10 (0.23), residues: 1257 helix: 1.38 (0.17), residues: 894 sheet: -1.50 (0.69), residues: 39 loop : -0.71 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 26 TYR 0.020 0.001 TYR A 405 PHE 0.028 0.001 PHE A1583 TRP 0.017 0.001 TRP A1245 HIS 0.005 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (11335) covalent geometry : angle 0.66326 / 0.33 (15300) SS BOND : bond 0.00373 / 0.27 ( 6) SS BOND : angle 1.70148 / 1.26 ( 12) hydrogen bonds : bond 0.04096 / 2.63 ( 708) hydrogen bonds : angle 4.45850 / 3.17 ( 2031) link_BETA1-4 : bond 0.00601 / 0.36 ( 2) link_BETA1-4 : angle 2.94846 / 1.36 ( 6) link_NAG-ASN : bond 0.00892 / 0.62 ( 4) link_NAG-ASN : angle 3.95625 / 2.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.8017 (mpp80) cc_final: 0.7667 (mpp80) REVERT: A 92 ASN cc_start: 0.5718 (OUTLIER) cc_final: 0.5517 (m110) REVERT: A 147 ASN cc_start: 0.8439 (t0) cc_final: 0.7497 (p0) REVERT: A 297 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7593 (tp30) REVERT: A 791 MET cc_start: 0.7274 (tmm) cc_final: 0.6629 (tpt) REVERT: A 798 MET cc_start: 0.7422 (ttm) cc_final: 0.7140 (tmm) REVERT: A 903 CYS cc_start: 0.7213 (m) cc_final: 0.6883 (m) REVERT: A 1252 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.8019 (t) REVERT: A 1541 GLN cc_start: 0.7689 (mp10) cc_final: 0.7400 (mm-40) REVERT: A 1609 PHE cc_start: 0.8118 (t80) cc_final: 0.7883 (t80) outliers start: 19 outliers final: 10 residues processed: 189 average time/residue: 0.4078 time to fit residues: 85.5306 Evaluate side-chains 177 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 1181 ILE Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1252 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN A1761 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.182383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.143975 restraints weight = 31525.873| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 6.52 r_work: 0.3104 rms_B_bonded: 6.24 restraints_weight: 2.0000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 11347 Z= 0.144 Angle : 0.689 13.934 15330 Z= 0.344 Chirality : 0.044 0.299 1726 Planarity : 0.004 0.050 1774 Dihedral : 14.650 173.756 2396 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.03 % Allowed : 19.95 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1257 helix: 1.36 (0.17), residues: 895 sheet: -1.47 (0.71), residues: 39 loop : -0.68 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1293 TYR 0.021 0.002 TYR A 405 PHE 0.026 0.001 PHE A1583 TRP 0.014 0.001 TRP A1245 HIS 0.005 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (11335) covalent geometry : angle 0.67694 / 0.34 (15300) SS BOND : bond 0.00270 / 0.22 ( 6) SS BOND : angle 1.65145 / 1.09 ( 12) hydrogen bonds : bond 0.04208 / 2.70 ( 708) hydrogen bonds : angle 4.49491 / 3.21 ( 2031) link_BETA1-4 : bond 0.00429 / 0.26 ( 2) link_BETA1-4 : angle 2.96444 / 1.36 ( 6) link_NAG-ASN : bond 0.00885 / 0.61 ( 4) link_NAG-ASN : angle 3.97205 / 2.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8816 (mt) cc_final: 0.8589 (mm) REVERT: A 147 ASN cc_start: 0.8493 (t0) cc_final: 0.7532 (p0) REVERT: A 297 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7578 (tp30) REVERT: A 326 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8479 (mt-10) REVERT: A 791 MET cc_start: 0.7275 (tmm) cc_final: 0.6641 (tpt) REVERT: A 798 MET cc_start: 0.7492 (ttm) cc_final: 0.7167 (tmm) REVERT: A 903 CYS cc_start: 0.7399 (m) cc_final: 0.7045 (m) REVERT: A 1252 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.8024 (t) REVERT: A 1541 GLN cc_start: 0.7708 (mp10) cc_final: 0.7451 (mm-40) REVERT: A 1548 TYR cc_start: 0.8967 (t80) cc_final: 0.8355 (t80) REVERT: A 1609 PHE cc_start: 0.8170 (t80) cc_final: 0.7934 (t80) outliers start: 22 outliers final: 13 residues processed: 179 average time/residue: 0.3860 time to fit residues: 76.8884 Evaluate side-chains 178 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 1181 ILE Chi-restraints excluded: chain A residue 1230 ASP Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1252 THR Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1761 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 84 optimal weight: 0.0980 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.181661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.139188 restraints weight = 28129.441| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 6.03 r_work: 0.3116 rms_B_bonded: 5.34 restraints_weight: 2.0000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11347 Z= 0.223 Angle : 0.738 14.533 15330 Z= 0.369 Chirality : 0.046 0.298 1726 Planarity : 0.005 0.051 1774 Dihedral : 14.794 175.055 2396 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.68 % Allowed : 20.30 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.23), residues: 1257 helix: 1.19 (0.17), residues: 896 sheet: -1.46 (0.71), residues: 39 loop : -0.71 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1293 TYR 0.026 0.002 TYR A 405 PHE 0.026 0.002 PHE A 971 TRP 0.012 0.002 TRP A1408 HIS 0.007 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.22 (11335) covalent geometry : angle 0.72528 / 0.37 (15300) SS BOND : bond 0.00227 / 0.18 ( 6) SS BOND : angle 1.91834 / 1.18 ( 12) hydrogen bonds : bond 0.04611 / 2.96 ( 708) hydrogen bonds : angle 4.61888 / 3.30 ( 2031) link_BETA1-4 : bond 0.00542 / 0.33 ( 2) link_BETA1-4 : angle 3.05775 / 1.43 ( 6) link_NAG-ASN : bond 0.00912 / 0.61 ( 4) link_NAG-ASN : angle 4.09837 / 2.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8543 (t0) cc_final: 0.7637 (p0) REVERT: A 297 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7582 (tp30) REVERT: A 791 MET cc_start: 0.7303 (tmm) cc_final: 0.6728 (tpt) REVERT: A 798 MET cc_start: 0.7467 (ttm) cc_final: 0.7180 (tmm) REVERT: A 903 CYS cc_start: 0.7294 (m) cc_final: 0.6942 (m) REVERT: A 1252 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7964 (t) REVERT: A 1541 GLN cc_start: 0.7687 (mp10) cc_final: 0.7486 (mm-40) REVERT: A 1548 TYR cc_start: 0.8951 (t80) cc_final: 0.8343 (t80) REVERT: A 1609 PHE cc_start: 0.8133 (t80) cc_final: 0.7889 (t80) outliers start: 18 outliers final: 13 residues processed: 170 average time/residue: 0.4026 time to fit residues: 75.9428 Evaluate side-chains 172 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 1181 ILE Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1252 THR Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1633 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 121 optimal weight: 0.3980 chunk 112 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.182489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124521 restraints weight = 23385.833| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.82 r_work: 0.3291 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11347 Z= 0.140 Angle : 0.698 15.264 15330 Z= 0.347 Chirality : 0.044 0.293 1726 Planarity : 0.004 0.051 1774 Dihedral : 14.237 167.076 2396 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.50 % Allowed : 20.65 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.05 (0.23), residues: 1257 helix: 1.33 (0.17), residues: 895 sheet: -1.41 (0.71), residues: 39 loop : -0.69 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 835 TYR 0.022 0.001 TYR A 405 PHE 0.024 0.001 PHE A 971 TRP 0.013 0.001 TRP A1245 HIS 0.006 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (11335) covalent geometry : angle 0.68521 / 0.34 (15300) SS BOND : bond 0.00296 / 0.24 ( 6) SS BOND : angle 1.57600 / 1.05 ( 12) hydrogen bonds : bond 0.04228 / 2.71 ( 708) hydrogen bonds : angle 4.50509 / 3.22 ( 2031) link_BETA1-4 : bond 0.00526 / 0.32 ( 2) link_BETA1-4 : angle 2.99718 / 1.38 ( 6) link_NAG-ASN : bond 0.00886 / 0.61 ( 4) link_NAG-ASN : angle 4.02441 / 2.56 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: A 26 ARG cc_start: 0.8140 (mpp80) cc_final: 0.7786 (mpp80) REVERT: A 147 ASN cc_start: 0.8347 (t0) cc_final: 0.7546 (p0) REVERT: A 297 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7653 (tp30) REVERT: A 791 MET cc_start: 0.7273 (tmm) cc_final: 0.6600 (tpt) REVERT: A 798 MET cc_start: 0.7400 (ttm) cc_final: 0.7171 (tmm) REVERT: A 903 CYS cc_start: 0.7179 (m) cc_final: 0.6766 (m) REVERT: A 1252 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7968 (t) REVERT: A 1548 TYR cc_start: 0.8868 (t80) cc_final: 0.8156 (t80) outliers start: 16 outliers final: 11 residues processed: 178 average time/residue: 0.4129 time to fit residues: 81.3848 Evaluate side-chains 172 residues out of total 1131 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 1181 ILE Chi-restraints excluded: chain A residue 1239 LEU Chi-restraints excluded: chain A residue 1252 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 100 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 29 optimal weight: 0.0370 chunk 113 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 chunk 64 optimal weight: 0.3980 chunk 108 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 757 ASN ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN A1761 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.179691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.132403 restraints weight = 17298.979| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 3.58 r_work: 0.3172 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11347 Z= 0.135 Angle : 0.702 17.121 15330 Z= 0.347 Chirality : 0.043 0.305 1726 Planarity : 0.004 0.049 1774 Dihedral : 13.685 157.850 2396 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.41 % Allowed : 20.39 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1257 helix: 1.36 (0.17), residues: 896 sheet: -1.35 (0.71), residues: 39 loop : -0.65 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 835 TYR 0.021 0.001 TYR A 405 PHE 0.028 0.001 PHE A1583 TRP 0.014 0.001 TRP A1245 HIS 0.004 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (11335) covalent geometry : angle 0.68941 / 0.34 (15300) SS BOND : bond 0.00279 / 0.23 ( 6) SS BOND : angle 1.55815 / 1.07 ( 12) hydrogen bonds : bond 0.04151 / 2.67 ( 708) hydrogen bonds : angle 4.51076 / 3.23 ( 2031) link_BETA1-4 : bond 0.00478 / 0.30 ( 2) link_BETA1-4 : angle 2.95824 / 1.36 ( 6) link_NAG-ASN : bond 0.00831 / 0.57 ( 4) link_NAG-ASN : angle 4.03518 / 2.60 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3690.76 seconds wall clock time: 63 minutes 38.41 seconds (3818.41 seconds total)