Starting phenix.real_space_refine on Thu Mar 5 04:34:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6p_28887/03_2026/8f6p_28887_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6p_28887/03_2026/8f6p_28887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8f6p_28887/03_2026/8f6p_28887_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6p_28887/03_2026/8f6p_28887_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f6p_28887/03_2026/8f6p_28887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6p_28887/03_2026/8f6p_28887.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.092 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 6 5.49 5 S 60 5.16 5 C 6250 2.51 5 N 1360 2.21 5 O 1602 1.98 5 H 8229 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17507 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 16596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1091, 16596 Classifications: {'peptide': 1091} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 1065} Chain breaks: 7 Unresolved non-hydrogen bonds: 424 Unresolved non-hydrogen angles: 536 Unresolved non-hydrogen dihedrals: 362 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'HIS:plan': 3, 'ARG:plan': 8, 'PHE:plan': 9, 'ASP:plan': 10, 'ASN:plan1': 6, 'GLU:plan': 13, 'GLN:plan1': 5, 'TYR:plan': 4, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 275 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: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 855 Unusual residues: {'6OU': 6, 'BMA': 3, 'NAG': 7, 'XHO': 1, 'Y01': 13} Classifications: {'undetermined': 30} Link IDs: {None: 29} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'6OU:plan-1': 2, 'Y01:plan-1': 1, 'Y01:plan-2': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 3.49, per 1000 atoms: 0.20 Number of scatterers: 17507 At special positions: 0 Unit cell: (112.992, 123.552, 105.6, 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 60 16.00 P 6 15.00 O 1602 8.00 N 1360 7.00 C 6250 6.00 H 8229 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 327 " distance=2.03 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 918 " distance=2.03 Simple disulfide: pdb=" SG CYS A1365 " - pdb=" SG CYS A1386 " distance=2.03 Simple disulfide: pdb=" SG CYS A1730 " - pdb=" SG CYS A1744 " 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 A2201 " - " ASN A 284 " " NAG A2208 " - " ASN A1376 " " NAG C 1 " - " ASN A1382 " Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 483.9 milliseconds 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2056 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 2 sheets defined 79.4% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 119 through 131 removed outlier: 3.702A pdb=" N ARG A 123 " --> pdb=" O HIS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 150 removed outlier: 3.718A pdb=" N SER A 135 " --> pdb=" O HIS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 180 removed outlier: 3.956A pdb=" N LYS A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR A 160 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 161 " --> pdb=" O TRP A 157 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 211 removed outlier: 3.639A pdb=" N ASP A 198 " --> pdb=" O TRP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 234 through 251 Processing helix chain 'A' and resid 251 through 273 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 312 through 315 removed outlier: 3.722A pdb=" N TYR A 315 " --> pdb=" O PRO A 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 315' Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 358 through 371 Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.936A pdb=" N LEU A 378 " --> pdb=" O CYS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 390 through 399 removed outlier: 3.628A pdb=" N PHE A 394 " --> pdb=" O TYR A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 430 Processing helix chain 'A' and resid 719 through 737 removed outlier: 3.868A pdb=" N THR A 723 " --> pdb=" O PHE A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 772 removed outlier: 3.679A pdb=" N LEU A 772 " --> pdb=" O LYS A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 778 Processing helix chain 'A' and resid 780 through 798 Processing helix chain 'A' and resid 806 through 808 No H-bonds generated for 'chain 'A' and resid 806 through 808' Processing helix chain 'A' and resid 809 through 814 removed outlier: 4.192A pdb=" N LEU A 813 " --> pdb=" O ARG A 809 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU A 814 " --> pdb=" O SER A 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 809 through 814' Processing helix chain 'A' and resid 815 through 822 removed outlier: 3.799A pdb=" N SER A 822 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 837 removed outlier: 3.625A pdb=" N VAL A 837 " --> pdb=" O ILE A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 869 removed outlier: 3.524A pdb=" N THR A 844 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LYS A 864 " --> pdb=" O GLN A 860 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ASN A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 874 removed outlier: 4.281A pdb=" N ILE A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 900 Processing helix chain 'A' and resid 903 through 913 removed outlier: 3.972A pdb=" N ASP A 908 " --> pdb=" O GLU A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 945 Processing helix chain 'A' and resid 1194 through 1206 Processing helix chain 'A' and resid 1206 through 1225 Processing helix chain 'A' and resid 1235 through 1270 removed outlier: 6.741A pdb=" N PHE A1265 " --> pdb=" O VAL A1261 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N LYS A1266 " --> pdb=" O ALA A1262 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS A1267 " --> pdb=" O TYR A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1292 Processing helix chain 'A' and resid 1302 through 1306 removed outlier: 3.737A pdb=" N THR A1306 " --> pdb=" O LYS A1302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1302 through 1306' Processing helix chain 'A' and resid 1307 through 1316 Proline residue: A1312 - end of helix Processing helix chain 'A' and resid 1319 through 1359 Proline residue: A1334 - end of helix removed outlier: 3.710A pdb=" N ILE A1349 " --> pdb=" O ILE A1345 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE A1350 " --> pdb=" O PHE A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1389 Processing helix chain 'A' and resid 1407 through 1419 Processing helix chain 'A' and resid 1422 through 1431 removed outlier: 3.823A pdb=" N ILE A1426 " --> pdb=" O GLY A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1459 removed outlier: 4.079A pdb=" N TYR A1451 " --> pdb=" O TYR A1447 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A1452 " --> pdb=" O MET A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1460 through 1482 Processing helix chain 'A' and resid 1490 through 1505 removed outlier: 3.598A pdb=" N SER A1505 " --> pdb=" O LYS A1501 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1528 removed outlier: 3.556A pdb=" N THR A1528 " --> pdb=" O PHE A1524 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1549 removed outlier: 3.771A pdb=" N ASP A1533 " --> pdb=" O LYS A1529 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A1549 " --> pdb=" O VAL A1545 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1582 Processing helix chain 'A' and resid 1585 through 1591 removed outlier: 3.775A pdb=" N PHE A1589 " --> pdb=" O ARG A1585 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN A1591 " --> pdb=" O TYR A1587 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1612 removed outlier: 3.721A pdb=" N ILE A1595 " --> pdb=" O ASN A1591 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A1612 " --> pdb=" O THR A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1623 through 1630 Processing helix chain 'A' and resid 1631 through 1641 Processing helix chain 'A' and resid 1643 through 1681 Proline residue: A1657 - end of helix Processing helix chain 'A' and resid 1698 through 1711 removed outlier: 4.219A pdb=" N THR A1711 " --> pdb=" O PHE A1707 " (cutoff:3.500A) Processing helix chain 'A' and resid 1714 through 1724 removed outlier: 3.502A pdb=" N LEU A1718 " --> pdb=" O GLY A1714 " (cutoff:3.500A) Proline residue: A1721 - end of helix removed outlier: 3.616A pdb=" N ASN A1724 " --> pdb=" O SER A1720 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1780 removed outlier: 3.734A pdb=" N TYR A1769 " --> pdb=" O VAL A1765 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 280 through 283 Processing sheet with id=AA2, first strand: chain 'A' and resid 1363 through 1367 609 hydrogen bonds defined for protein. 1734 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: 4.23 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8218 1.03 - 1.23: 37 1.23 - 1.42: 3719 1.42 - 1.61: 5637 1.61 - 1.81: 119 Bond restraints: 17730 Sorted by residual: bond pdb=" CAS Y01 A2229 " pdb=" CAU Y01 A2229 " ideal model delta sigma weight residual 1.530 1.654 -0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" CAL Y01 A2229 " pdb=" CAX Y01 A2229 " ideal model delta sigma weight residual 1.540 1.664 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" CAI Y01 A2229 " pdb=" CAK Y01 A2229 " ideal model delta sigma weight residual 1.492 1.373 0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" C16 6OU A2217 " pdb=" O18 6OU A2217 " ideal model delta sigma weight residual 1.327 1.446 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C16 6OU A2212 " pdb=" O18 6OU A2212 " ideal model delta sigma weight residual 1.327 1.445 -0.118 2.00e-02 2.50e+03 3.51e+01 ... (remaining 17725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.28: 31410 5.28 - 10.56: 113 10.56 - 15.85: 25 15.85 - 21.13: 6 21.13 - 26.41: 4 Bond angle restraints: 31558 Sorted by residual: angle pdb=" C40 6OU A2216 " pdb=" C41 6OU A2216 " pdb=" C42 6OU A2216 " ideal model delta sigma weight residual 127.56 153.97 -26.41 3.00e+00 1.11e-01 7.75e+01 angle pdb=" C40 6OU A2213 " pdb=" C41 6OU A2213 " pdb=" C42 6OU A2213 " ideal model delta sigma weight residual 127.56 153.85 -26.29 3.00e+00 1.11e-01 7.68e+01 angle pdb=" C40 6OU A2214 " pdb=" C41 6OU A2214 " pdb=" C42 6OU A2214 " ideal model delta sigma weight residual 127.56 153.19 -25.63 3.00e+00 1.11e-01 7.30e+01 angle pdb=" C40 6OU A2212 " pdb=" C41 6OU A2212 " pdb=" C42 6OU A2212 " ideal model delta sigma weight residual 127.56 152.90 -25.34 3.00e+00 1.11e-01 7.14e+01 angle pdb=" CAM Y01 A2229 " pdb=" CAY Y01 A2229 " pdb=" OAW Y01 A2229 " ideal model delta sigma weight residual 111.19 128.75 -17.56 3.00e+00 1.11e-01 3.43e+01 ... (remaining 31553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.98: 8885 31.98 - 63.96: 404 63.96 - 95.95: 57 95.95 - 127.93: 27 127.93 - 159.91: 4 Dihedral angle restraints: 9377 sinusoidal: 5501 harmonic: 3876 Sorted by residual: dihedral pdb=" CB CYS A 909 " pdb=" SG CYS A 909 " pdb=" SG CYS A 918 " pdb=" CB CYS A 918 " ideal model delta sinusoidal sigma weight residual 93.00 142.19 -49.19 1 1.00e+01 1.00e-02 3.33e+01 dihedral pdb=" CB CYS A 281 " pdb=" SG CYS A 281 " pdb=" SG CYS A 327 " pdb=" CB CYS A 327 " ideal model delta sinusoidal sigma weight residual -86.00 -134.71 48.71 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" C19 6OU A2215 " pdb=" C20 6OU A2215 " pdb=" C21 6OU A2215 " pdb=" O22 6OU A2215 " ideal model delta sinusoidal sigma weight residual -59.00 100.91 -159.91 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 9374 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 1498 0.121 - 0.241: 55 0.241 - 0.362: 4 0.362 - 0.482: 1 0.482 - 0.603: 1 Chirality restraints: 1559 Sorted by residual: chirality pdb=" C20 XHO A2211 " pdb=" C19 XHO A2211 " pdb=" C21 XHO A2211 " pdb=" O31 XHO A2211 " both_signs ideal model delta sigma weight residual False 2.20 2.80 -0.60 2.00e-01 2.50e+01 9.08e+00 chirality pdb=" C1 NAG A2201 " pdb=" ND2 ASN A 284 " pdb=" C2 NAG A2201 " pdb=" O5 NAG A2201 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" CBH Y01 A2229 " pdb=" CAT Y01 A2229 " pdb=" CAZ Y01 A2229 " pdb=" CBF Y01 A2229 " both_signs ideal model delta sigma weight residual False -2.85 -2.53 -0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 1556 not shown) Planarity restraints: 2540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A1764 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00 pdb=" C ILE A1764 " -0.035 2.00e-02 2.50e+03 pdb=" O ILE A1764 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL A1765 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1763 " 0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C LEU A1763 " -0.030 2.00e-02 2.50e+03 pdb=" O LEU A1763 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A1764 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A1439 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO A1440 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A1440 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1440 " -0.023 5.00e-02 4.00e+02 ... (remaining 2537 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 665 2.17 - 2.78: 32561 2.78 - 3.38: 48319 3.38 - 3.99: 60401 3.99 - 4.60: 95868 Nonbonded interactions: 237814 Sorted by model distance: nonbonded pdb=" OD1 ASN A 284 " pdb=" H ASN A 284 " model vdw 1.561 2.450 nonbonded pdb=" OD1 ASN A1381 " pdb="HH22 ARG A1434 " model vdw 1.646 2.450 nonbonded pdb="HE21 GLN A 372 " pdb=" OG SER A 402 " model vdw 1.669 2.450 nonbonded pdb=" O ASN A1381 " pdb=" H GLN A1439 " model vdw 1.676 2.450 nonbonded pdb=" OD1 ASP A 886 " pdb=" H PHE A 887 " model vdw 1.739 2.450 ... (remaining 237809 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.500 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.124 9510 Z= 0.514 Angle : 1.344 26.411 12954 Z= 0.495 Chirality : 0.053 0.603 1559 Planarity : 0.003 0.041 1478 Dihedral : 19.794 159.911 4347 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.12 % Allowed : 0.35 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.26), residues: 1075 helix: 2.01 (0.19), residues: 751 sheet: -3.34 (1.22), residues: 14 loop : -0.30 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1305 TYR 0.017 0.001 TYR A 379 PHE 0.015 0.001 PHE A1753 TRP 0.022 0.001 TRP A1423 HIS 0.003 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.01038 ( 9501) covalent geometry : angle 1.33362 (12931) SS BOND : bond 0.00335 ( 4) SS BOND : angle 1.36365 ( 8) hydrogen bonds : bond 0.11062 ( 609) hydrogen bonds : angle 5.02745 ( 1734) link_BETA1-4 : bond 0.01401 ( 2) link_BETA1-4 : angle 5.95753 ( 6) link_NAG-ASN : bond 0.00943 ( 3) link_NAG-ASN : angle 4.49106 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 127 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue SER 235 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue SER 355 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue THR 428 is missing expected H atoms. Skipping. Residue MET 726 is missing expected H atoms. Skipping. Residue VAL 752 is missing expected H atoms. Skipping. Residue LEU 755 is missing expected H atoms. Skipping. Residue MET 765 is missing expected H atoms. Skipping. Residue THR 766 is missing expected H atoms. Skipping. Residue ILE 769 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue TYR 775 is missing expected H atoms. Skipping. Residue TYR 776 is missing expected H atoms. Skipping. Residue TYR 777 is missing expected H atoms. Skipping. Residue ILE 788 is missing expected H atoms. Skipping. Residue ILE 791 is missing expected H atoms. Skipping. Residue LEU 792 is missing expected H atoms. Skipping. Residue SER 793 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue MET 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue LEU 808 is missing expected H atoms. Skipping. Residue SER 876 is missing expected H atoms. Skipping. Residue LEU 878 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue LYS 1302 is missing expected H atoms. Skipping. Residue MET 1499 is missing expected H atoms. Skipping. Residue LYS 1506 is missing expected H atoms. Skipping. Residue LYS 1507 is missing expected H atoms. Skipping. Residue ILE 1526 is missing expected H atoms. Skipping. Residue LYS 1529 is missing expected H atoms. Skipping. Residue TYR 1587 is missing expected H atoms. Skipping. Residue TYR 1588 is missing expected H atoms. Skipping. Residue THR 1590 is missing expected H atoms. Skipping. Residue ILE 1613 is missing expected H atoms. Skipping. Residue VAL 1626 is missing expected H atoms. Skipping. Residue ILE 1627 is missing expected H atoms. Skipping. Residue SER 1737 is missing expected H atoms. Skipping. Residue SER 1740 is missing expected H atoms. Skipping. Residue TYR 1769 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.8405 (m-80) cc_final: 0.8197 (m-80) REVERT: A 723 THR cc_start: 0.8252 (m) cc_final: 0.7802 (m) REVERT: A 1572 ILE cc_start: 0.8405 (mt) cc_final: 0.8203 (mt) outliers start: 1 outliers final: 1 residues processed: 177 average time/residue: 0.1848 time to fit residues: 48.1218 Evaluate side-chains 164 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 915 GLN ** 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 = 0.3834 r_free = 0.3834 target = 0.158507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.122246 restraints weight = 30807.564| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.97 r_work: 0.3251 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9510 Z= 0.125 Angle : 0.555 8.128 12954 Z= 0.270 Chirality : 0.036 0.299 1559 Planarity : 0.003 0.038 1478 Dihedral : 16.654 157.612 2601 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.71 % Allowed : 6.82 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.19 (0.26), residues: 1075 helix: 2.26 (0.19), residues: 755 sheet: -3.70 (1.12), residues: 14 loop : -0.34 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1434 TYR 0.015 0.001 TYR A 379 PHE 0.016 0.001 PHE A1455 TRP 0.023 0.001 TRP A1423 HIS 0.002 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9501) covalent geometry : angle 0.53480 (12931) SS BOND : bond 0.00238 ( 4) SS BOND : angle 0.82645 ( 8) hydrogen bonds : bond 0.03881 ( 609) hydrogen bonds : angle 3.99644 ( 1734) link_BETA1-4 : bond 0.00330 ( 2) link_BETA1-4 : angle 2.30997 ( 6) link_NAG-ASN : bond 0.00988 ( 3) link_NAG-ASN : angle 5.28550 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 127 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue SER 235 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue SER 355 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue THR 428 is missing expected H atoms. Skipping. Residue MET 726 is missing expected H atoms. Skipping. Residue VAL 752 is missing expected H atoms. Skipping. Residue LEU 755 is missing expected H atoms. Skipping. Residue MET 765 is missing expected H atoms. Skipping. Residue THR 766 is missing expected H atoms. Skipping. Residue ILE 769 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue TYR 775 is missing expected H atoms. Skipping. Residue TYR 776 is missing expected H atoms. Skipping. Residue TYR 777 is missing expected H atoms. Skipping. Residue ILE 788 is missing expected H atoms. Skipping. Residue ILE 791 is missing expected H atoms. Skipping. Residue LEU 792 is missing expected H atoms. Skipping. Residue SER 793 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue MET 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue LEU 808 is missing expected H atoms. Skipping. Residue SER 876 is missing expected H atoms. Skipping. Residue LEU 878 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue LYS 1302 is missing expected H atoms. Skipping. Residue MET 1499 is missing expected H atoms. Skipping. Residue LYS 1506 is missing expected H atoms. Skipping. Residue LYS 1507 is missing expected H atoms. Skipping. Residue ILE 1526 is missing expected H atoms. Skipping. Residue LYS 1529 is missing expected H atoms. Skipping. Residue TYR 1587 is missing expected H atoms. Skipping. Residue TYR 1588 is missing expected H atoms. Skipping. Residue THR 1590 is missing expected H atoms. Skipping. Residue ILE 1613 is missing expected H atoms. Skipping. Residue VAL 1626 is missing expected H atoms. Skipping. Residue ILE 1627 is missing expected H atoms. Skipping. Residue SER 1737 is missing expected H atoms. Skipping. Residue SER 1740 is missing expected H atoms. Skipping. Residue TYR 1769 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 170 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1411 TYR cc_start: 0.8813 (m-80) cc_final: 0.8513 (m-80) REVERT: A 1572 ILE cc_start: 0.8249 (mt) cc_final: 0.8043 (mt) outliers start: 6 outliers final: 6 residues processed: 172 average time/residue: 0.1873 time to fit residues: 47.3342 Evaluate side-chains 168 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 162 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1343 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 39 optimal weight: 3.9990 chunk 63 optimal weight: 0.0970 chunk 30 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1477 GLN ** A1695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.158375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.119890 restraints weight = 31398.637| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.06 r_work: 0.3228 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9510 Z= 0.169 Angle : 0.547 9.229 12954 Z= 0.271 Chirality : 0.035 0.291 1559 Planarity : 0.003 0.039 1478 Dihedral : 14.885 164.649 2601 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.82 % Allowed : 8.94 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.16 (0.26), residues: 1075 helix: 2.20 (0.18), residues: 765 sheet: -3.58 (1.15), residues: 14 loop : -0.35 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1364 TYR 0.019 0.001 TYR A 379 PHE 0.014 0.001 PHE A1753 TRP 0.019 0.001 TRP A1423 HIS 0.002 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9501) covalent geometry : angle 0.53053 (12931) SS BOND : bond 0.00355 ( 4) SS BOND : angle 0.85412 ( 8) hydrogen bonds : bond 0.03932 ( 609) hydrogen bonds : angle 3.94100 ( 1734) link_BETA1-4 : bond 0.00164 ( 2) link_BETA1-4 : angle 1.78407 ( 6) link_NAG-ASN : bond 0.01031 ( 3) link_NAG-ASN : angle 4.86273 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 127 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue SER 235 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue SER 355 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue THR 428 is missing expected H atoms. Skipping. Residue MET 726 is missing expected H atoms. Skipping. Residue VAL 752 is missing expected H atoms. Skipping. Residue LEU 755 is missing expected H atoms. Skipping. Residue MET 765 is missing expected H atoms. Skipping. Residue THR 766 is missing expected H atoms. Skipping. Residue ILE 769 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue TYR 775 is missing expected H atoms. Skipping. Residue TYR 776 is missing expected H atoms. Skipping. Residue TYR 777 is missing expected H atoms. Skipping. Residue ILE 788 is missing expected H atoms. Skipping. Residue ILE 791 is missing expected H atoms. Skipping. Residue LEU 792 is missing expected H atoms. Skipping. Residue SER 793 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue MET 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue LEU 808 is missing expected H atoms. Skipping. Residue SER 876 is missing expected H atoms. Skipping. Residue LEU 878 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue LYS 1302 is missing expected H atoms. Skipping. Residue MET 1499 is missing expected H atoms. Skipping. Residue LYS 1506 is missing expected H atoms. Skipping. Residue LYS 1507 is missing expected H atoms. Skipping. Residue ILE 1526 is missing expected H atoms. Skipping. Residue LYS 1529 is missing expected H atoms. Skipping. Residue TYR 1587 is missing expected H atoms. Skipping. Residue TYR 1588 is missing expected H atoms. Skipping. Residue THR 1590 is missing expected H atoms. Skipping. Residue ILE 1613 is missing expected H atoms. Skipping. Residue VAL 1626 is missing expected H atoms. Skipping. Residue ILE 1627 is missing expected H atoms. Skipping. Residue SER 1737 is missing expected H atoms. Skipping. Residue SER 1740 is missing expected H atoms. Skipping. Residue TYR 1769 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 165 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1248 PHE cc_start: 0.7854 (m-80) cc_final: 0.7572 (m-80) REVERT: A 1411 TYR cc_start: 0.8921 (m-80) cc_final: 0.8565 (m-80) REVERT: A 1477 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.6649 (mp-120) outliers start: 7 outliers final: 6 residues processed: 168 average time/residue: 0.1783 time to fit residues: 43.8785 Evaluate side-chains 165 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 158 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1343 CYS Chi-restraints excluded: chain A residue 1477 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 915 GLN ** 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 = 0.3856 r_free = 0.3856 target = 0.160041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121725 restraints weight = 31216.676| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.06 r_work: 0.3253 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9510 Z= 0.114 Angle : 0.493 8.016 12954 Z= 0.249 Chirality : 0.034 0.264 1559 Planarity : 0.003 0.039 1478 Dihedral : 13.750 178.109 2601 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.82 % Allowed : 9.88 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.25 (0.26), residues: 1075 helix: 2.28 (0.18), residues: 765 sheet: -3.62 (1.14), residues: 14 loop : -0.34 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 815 TYR 0.014 0.001 TYR A 379 PHE 0.014 0.001 PHE A1753 TRP 0.010 0.001 TRP A1423 HIS 0.002 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9501) covalent geometry : angle 0.47783 (12931) SS BOND : bond 0.00309 ( 4) SS BOND : angle 0.73839 ( 8) hydrogen bonds : bond 0.03648 ( 609) hydrogen bonds : angle 3.79621 ( 1734) link_BETA1-4 : bond 0.00126 ( 2) link_BETA1-4 : angle 1.54462 ( 6) link_NAG-ASN : bond 0.01035 ( 3) link_NAG-ASN : angle 4.51501 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 127 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue SER 235 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue SER 355 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue THR 428 is missing expected H atoms. Skipping. Residue MET 726 is missing expected H atoms. Skipping. Residue VAL 752 is missing expected H atoms. Skipping. Residue LEU 755 is missing expected H atoms. Skipping. Residue MET 765 is missing expected H atoms. Skipping. Residue THR 766 is missing expected H atoms. Skipping. Residue ILE 769 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue TYR 775 is missing expected H atoms. Skipping. Residue TYR 776 is missing expected H atoms. Skipping. Residue TYR 777 is missing expected H atoms. Skipping. Residue ILE 788 is missing expected H atoms. Skipping. Residue ILE 791 is missing expected H atoms. Skipping. Residue LEU 792 is missing expected H atoms. Skipping. Residue SER 793 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue MET 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue LEU 808 is missing expected H atoms. Skipping. Residue SER 876 is missing expected H atoms. Skipping. Residue LEU 878 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue LYS 1302 is missing expected H atoms. Skipping. Residue MET 1499 is missing expected H atoms. Skipping. Residue LYS 1506 is missing expected H atoms. Skipping. Residue LYS 1507 is missing expected H atoms. Skipping. Residue ILE 1526 is missing expected H atoms. Skipping. Residue LYS 1529 is missing expected H atoms. Skipping. Residue TYR 1587 is missing expected H atoms. Skipping. Residue TYR 1588 is missing expected H atoms. Skipping. Residue THR 1590 is missing expected H atoms. Skipping. Residue ILE 1613 is missing expected H atoms. Skipping. Residue VAL 1626 is missing expected H atoms. Skipping. Residue ILE 1627 is missing expected H atoms. Skipping. Residue SER 1737 is missing expected H atoms. Skipping. Residue SER 1740 is missing expected H atoms. Skipping. Residue TYR 1769 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 164 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1411 TYR cc_start: 0.8919 (m-80) cc_final: 0.8701 (m-80) outliers start: 7 outliers final: 6 residues processed: 166 average time/residue: 0.1794 time to fit residues: 43.5966 Evaluate side-chains 165 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1343 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 80 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 915 GLN ** 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 = 0.3850 r_free = 0.3850 target = 0.159334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.120952 restraints weight = 31070.658| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.05 r_work: 0.3243 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9510 Z= 0.126 Angle : 0.497 8.114 12954 Z= 0.249 Chirality : 0.034 0.264 1559 Planarity : 0.003 0.039 1478 Dihedral : 12.410 141.748 2599 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.53 % Allowed : 9.76 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.34 (0.26), residues: 1075 helix: 2.35 (0.18), residues: 766 sheet: -3.51 (1.18), residues: 14 loop : -0.34 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 815 TYR 0.016 0.001 TYR A 379 PHE 0.014 0.001 PHE A1753 TRP 0.011 0.001 TRP A1423 HIS 0.002 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9501) covalent geometry : angle 0.48238 (12931) SS BOND : bond 0.00326 ( 4) SS BOND : angle 0.77002 ( 8) hydrogen bonds : bond 0.03488 ( 609) hydrogen bonds : angle 3.71399 ( 1734) link_BETA1-4 : bond 0.00179 ( 2) link_BETA1-4 : angle 1.33651 ( 6) link_NAG-ASN : bond 0.00986 ( 3) link_NAG-ASN : angle 4.37716 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 127 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue SER 235 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue SER 355 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue THR 428 is missing expected H atoms. Skipping. Residue MET 726 is missing expected H atoms. Skipping. Residue VAL 752 is missing expected H atoms. Skipping. Residue LEU 755 is missing expected H atoms. Skipping. Residue MET 765 is missing expected H atoms. Skipping. Residue THR 766 is missing expected H atoms. Skipping. Residue ILE 769 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue TYR 775 is missing expected H atoms. Skipping. Residue TYR 776 is missing expected H atoms. Skipping. Residue TYR 777 is missing expected H atoms. Skipping. Residue ILE 788 is missing expected H atoms. Skipping. Residue ILE 791 is missing expected H atoms. Skipping. Residue LEU 792 is missing expected H atoms. Skipping. Residue SER 793 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue MET 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue LEU 808 is missing expected H atoms. Skipping. Residue SER 876 is missing expected H atoms. Skipping. Residue LEU 878 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue LYS 1302 is missing expected H atoms. Skipping. Residue MET 1499 is missing expected H atoms. Skipping. Residue LYS 1506 is missing expected H atoms. Skipping. Residue LYS 1507 is missing expected H atoms. Skipping. Residue ILE 1526 is missing expected H atoms. Skipping. Residue LYS 1529 is missing expected H atoms. Skipping. Residue TYR 1587 is missing expected H atoms. Skipping. Residue TYR 1588 is missing expected H atoms. Skipping. Residue THR 1590 is missing expected H atoms. Skipping. Residue ILE 1613 is missing expected H atoms. Skipping. Residue VAL 1626 is missing expected H atoms. Skipping. Residue ILE 1627 is missing expected H atoms. Skipping. Residue SER 1737 is missing expected H atoms. Skipping. Residue SER 1740 is missing expected H atoms. Skipping. Residue TYR 1769 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1364 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.7065 (mtt90) REVERT: A 1411 TYR cc_start: 0.8953 (m-80) cc_final: 0.8750 (m-80) outliers start: 13 outliers final: 11 residues processed: 163 average time/residue: 0.1933 time to fit residues: 45.4938 Evaluate side-chains 166 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 1206 HIS Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1343 CYS Chi-restraints excluded: chain A residue 1364 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 15 optimal weight: 0.0980 chunk 20 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 84 optimal weight: 0.0670 chunk 79 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 63 optimal weight: 0.0980 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 90 optimal weight: 10.0000 overall best weight: 0.2718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 915 GLN ** 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 = 0.3860 r_free = 0.3860 target = 0.160198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.124548 restraints weight = 30733.868| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.95 r_work: 0.3285 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9510 Z= 0.089 Angle : 0.452 7.833 12954 Z= 0.229 Chirality : 0.033 0.255 1559 Planarity : 0.003 0.037 1478 Dihedral : 11.245 115.266 2599 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.18 % Allowed : 10.71 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.54 (0.26), residues: 1075 helix: 2.52 (0.18), residues: 766 sheet: -3.54 (1.16), residues: 14 loop : -0.33 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 815 TYR 0.011 0.001 TYR A 379 PHE 0.014 0.001 PHE A1753 TRP 0.007 0.001 TRP A1442 HIS 0.001 0.000 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00186 ( 9501) covalent geometry : angle 0.43784 (12931) SS BOND : bond 0.00262 ( 4) SS BOND : angle 0.63507 ( 8) hydrogen bonds : bond 0.03245 ( 609) hydrogen bonds : angle 3.58777 ( 1734) link_BETA1-4 : bond 0.00111 ( 2) link_BETA1-4 : angle 1.28901 ( 6) link_NAG-ASN : bond 0.01073 ( 3) link_NAG-ASN : angle 4.12729 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 127 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue SER 235 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue SER 355 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue THR 428 is missing expected H atoms. Skipping. Residue MET 726 is missing expected H atoms. Skipping. Residue VAL 752 is missing expected H atoms. Skipping. Residue LEU 755 is missing expected H atoms. Skipping. Residue MET 765 is missing expected H atoms. Skipping. Residue THR 766 is missing expected H atoms. Skipping. Residue ILE 769 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue TYR 775 is missing expected H atoms. Skipping. Residue TYR 776 is missing expected H atoms. Skipping. Residue TYR 777 is missing expected H atoms. Skipping. Residue ILE 788 is missing expected H atoms. Skipping. Residue ILE 791 is missing expected H atoms. Skipping. Residue LEU 792 is missing expected H atoms. Skipping. Residue SER 793 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue MET 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue LEU 808 is missing expected H atoms. Skipping. Residue SER 876 is missing expected H atoms. Skipping. Residue LEU 878 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue LYS 1302 is missing expected H atoms. Skipping. Residue MET 1499 is missing expected H atoms. Skipping. Residue LYS 1506 is missing expected H atoms. Skipping. Residue LYS 1507 is missing expected H atoms. Skipping. Residue ILE 1526 is missing expected H atoms. Skipping. Residue LYS 1529 is missing expected H atoms. Skipping. Residue TYR 1587 is missing expected H atoms. Skipping. Residue TYR 1588 is missing expected H atoms. Skipping. Residue THR 1590 is missing expected H atoms. Skipping. Residue ILE 1613 is missing expected H atoms. Skipping. Residue VAL 1626 is missing expected H atoms. Skipping. Residue ILE 1627 is missing expected H atoms. Skipping. Residue SER 1737 is missing expected H atoms. Skipping. Residue SER 1740 is missing expected H atoms. Skipping. Residue TYR 1769 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.7780 (tpp) cc_final: 0.7463 (mtt) REVERT: A 207 THR cc_start: 0.8618 (m) cc_final: 0.8346 (p) outliers start: 10 outliers final: 8 residues processed: 165 average time/residue: 0.1895 time to fit residues: 45.4077 Evaluate side-chains 169 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 1206 HIS Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1629 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 30 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1695 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.158771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.120267 restraints weight = 31340.767| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.07 r_work: 0.3231 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9510 Z= 0.162 Angle : 0.504 7.944 12954 Z= 0.258 Chirality : 0.035 0.279 1559 Planarity : 0.004 0.125 1478 Dihedral : 11.358 125.773 2599 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.65 % Allowed : 10.59 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.44 (0.26), residues: 1075 helix: 2.43 (0.18), residues: 766 sheet: -3.31 (1.24), residues: 14 loop : -0.34 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1364 TYR 0.018 0.001 TYR A 379 PHE 0.013 0.001 PHE A1753 TRP 0.012 0.001 TRP A1423 HIS 0.012 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9501) covalent geometry : angle 0.49079 (12931) SS BOND : bond 0.00344 ( 4) SS BOND : angle 0.73654 ( 8) hydrogen bonds : bond 0.03511 ( 609) hydrogen bonds : angle 3.69171 ( 1734) link_BETA1-4 : bond 0.00172 ( 2) link_BETA1-4 : angle 1.25218 ( 6) link_NAG-ASN : bond 0.00959 ( 3) link_NAG-ASN : angle 4.26625 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 127 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue SER 235 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue SER 355 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue THR 428 is missing expected H atoms. Skipping. Residue MET 726 is missing expected H atoms. Skipping. Residue VAL 752 is missing expected H atoms. Skipping. Residue LEU 755 is missing expected H atoms. Skipping. Residue MET 765 is missing expected H atoms. Skipping. Residue THR 766 is missing expected H atoms. Skipping. Residue ILE 769 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue TYR 775 is missing expected H atoms. Skipping. Residue TYR 776 is missing expected H atoms. Skipping. Residue TYR 777 is missing expected H atoms. Skipping. Residue ILE 788 is missing expected H atoms. Skipping. Residue ILE 791 is missing expected H atoms. Skipping. Residue LEU 792 is missing expected H atoms. Skipping. Residue SER 793 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue MET 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue LEU 808 is missing expected H atoms. Skipping. Residue SER 876 is missing expected H atoms. Skipping. Residue LEU 878 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue LYS 1302 is missing expected H atoms. Skipping. Residue MET 1499 is missing expected H atoms. Skipping. Residue LYS 1506 is missing expected H atoms. Skipping. Residue LYS 1507 is missing expected H atoms. Skipping. Residue ILE 1526 is missing expected H atoms. Skipping. Residue LYS 1529 is missing expected H atoms. Skipping. Residue TYR 1587 is missing expected H atoms. Skipping. Residue TYR 1588 is missing expected H atoms. Skipping. Residue THR 1590 is missing expected H atoms. Skipping. Residue ILE 1613 is missing expected H atoms. Skipping. Residue VAL 1626 is missing expected H atoms. Skipping. Residue ILE 1627 is missing expected H atoms. Skipping. Residue SER 1737 is missing expected H atoms. Skipping. Residue SER 1740 is missing expected H atoms. Skipping. Residue TYR 1769 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.7877 (tpp) cc_final: 0.7477 (mtt) REVERT: A 207 THR cc_start: 0.8613 (m) cc_final: 0.8340 (p) outliers start: 14 outliers final: 11 residues processed: 164 average time/residue: 0.1897 time to fit residues: 45.2996 Evaluate side-chains 167 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 1206 HIS Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1343 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 20 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.158898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120496 restraints weight = 31081.864| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.06 r_work: 0.3220 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 0.034 9510 Z= 0.137 Angle : 0.487 7.893 12954 Z= 0.249 Chirality : 0.034 0.267 1559 Planarity : 0.003 0.041 1478 Dihedral : 11.101 120.678 2599 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.29 % Allowed : 11.76 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.32 (0.26), residues: 1075 helix: 2.39 (0.18), residues: 774 sheet: -3.53 (1.16), residues: 14 loop : -0.58 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1364 TYR 0.016 0.001 TYR A 379 PHE 0.014 0.001 PHE A1753 TRP 0.009 0.001 TRP A1423 HIS 0.009 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9501) covalent geometry : angle 0.47350 (12931) SS BOND : bond 0.00339 ( 4) SS BOND : angle 0.82304 ( 8) hydrogen bonds : bond 0.03444 ( 609) hydrogen bonds : angle 3.66098 ( 1734) link_BETA1-4 : bond 0.00193 ( 2) link_BETA1-4 : angle 1.24696 ( 6) link_NAG-ASN : bond 0.00962 ( 3) link_NAG-ASN : angle 4.14805 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 127 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue SER 235 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue SER 355 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue THR 428 is missing expected H atoms. Skipping. Residue MET 726 is missing expected H atoms. Skipping. Residue VAL 752 is missing expected H atoms. Skipping. Residue LEU 755 is missing expected H atoms. Skipping. Residue MET 765 is missing expected H atoms. Skipping. Residue THR 766 is missing expected H atoms. Skipping. Residue ILE 769 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue TYR 775 is missing expected H atoms. Skipping. Residue TYR 776 is missing expected H atoms. Skipping. Residue TYR 777 is missing expected H atoms. Skipping. Residue ILE 788 is missing expected H atoms. Skipping. Residue ILE 791 is missing expected H atoms. Skipping. Residue LEU 792 is missing expected H atoms. Skipping. Residue SER 793 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue MET 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue LEU 808 is missing expected H atoms. Skipping. Residue SER 876 is missing expected H atoms. Skipping. Residue LEU 878 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue LYS 1302 is missing expected H atoms. Skipping. Residue MET 1499 is missing expected H atoms. Skipping. Residue LYS 1506 is missing expected H atoms. Skipping. Residue LYS 1507 is missing expected H atoms. Skipping. Residue ILE 1526 is missing expected H atoms. Skipping. Residue LYS 1529 is missing expected H atoms. Skipping. Residue TYR 1587 is missing expected H atoms. Skipping. Residue TYR 1588 is missing expected H atoms. Skipping. Residue THR 1590 is missing expected H atoms. Skipping. Residue ILE 1613 is missing expected H atoms. Skipping. Residue VAL 1626 is missing expected H atoms. Skipping. Residue ILE 1627 is missing expected H atoms. Skipping. Residue SER 1737 is missing expected H atoms. Skipping. Residue SER 1740 is missing expected H atoms. Skipping. Residue TYR 1769 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.7873 (tpp) cc_final: 0.7611 (mtt) outliers start: 11 outliers final: 11 residues processed: 165 average time/residue: 0.1925 time to fit residues: 46.1162 Evaluate side-chains 170 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 1206 HIS Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1343 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.159835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.121579 restraints weight = 31113.224| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.06 r_work: 0.3232 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9510 Z= 0.111 Angle : 0.470 7.769 12954 Z= 0.240 Chirality : 0.033 0.259 1559 Planarity : 0.003 0.041 1478 Dihedral : 10.676 114.364 2599 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.18 % Allowed : 12.24 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.45 (0.26), residues: 1075 helix: 2.47 (0.18), residues: 768 sheet: -3.61 (1.10), residues: 14 loop : -0.43 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1364 TYR 0.014 0.001 TYR A 379 PHE 0.014 0.001 PHE A1753 TRP 0.008 0.001 TRP A1423 HIS 0.009 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9501) covalent geometry : angle 0.45715 (12931) SS BOND : bond 0.00316 ( 4) SS BOND : angle 0.72031 ( 8) hydrogen bonds : bond 0.03325 ( 609) hydrogen bonds : angle 3.61010 ( 1734) link_BETA1-4 : bond 0.00145 ( 2) link_BETA1-4 : angle 1.21043 ( 6) link_NAG-ASN : bond 0.00993 ( 3) link_NAG-ASN : angle 4.04376 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 127 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue SER 235 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue SER 355 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue THR 428 is missing expected H atoms. Skipping. Residue MET 726 is missing expected H atoms. Skipping. Residue VAL 752 is missing expected H atoms. Skipping. Residue LEU 755 is missing expected H atoms. Skipping. Residue MET 765 is missing expected H atoms. Skipping. Residue THR 766 is missing expected H atoms. Skipping. Residue ILE 769 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue TYR 775 is missing expected H atoms. Skipping. Residue TYR 776 is missing expected H atoms. Skipping. Residue TYR 777 is missing expected H atoms. Skipping. Residue ILE 788 is missing expected H atoms. Skipping. Residue ILE 791 is missing expected H atoms. Skipping. Residue LEU 792 is missing expected H atoms. Skipping. Residue SER 793 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue MET 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue LEU 808 is missing expected H atoms. Skipping. Residue SER 876 is missing expected H atoms. Skipping. Residue LEU 878 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue LYS 1302 is missing expected H atoms. Skipping. Residue MET 1499 is missing expected H atoms. Skipping. Residue LYS 1506 is missing expected H atoms. Skipping. Residue LYS 1507 is missing expected H atoms. Skipping. Residue ILE 1526 is missing expected H atoms. Skipping. Residue LYS 1529 is missing expected H atoms. Skipping. Residue TYR 1587 is missing expected H atoms. Skipping. Residue TYR 1588 is missing expected H atoms. Skipping. Residue THR 1590 is missing expected H atoms. Skipping. Residue ILE 1613 is missing expected H atoms. Skipping. Residue VAL 1626 is missing expected H atoms. Skipping. Residue ILE 1627 is missing expected H atoms. Skipping. Residue SER 1737 is missing expected H atoms. Skipping. Residue SER 1740 is missing expected H atoms. Skipping. Residue TYR 1769 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.7874 (tpp) cc_final: 0.7604 (mtt) outliers start: 10 outliers final: 10 residues processed: 165 average time/residue: 0.1774 time to fit residues: 42.3716 Evaluate side-chains 170 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 1206 HIS Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1343 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1695 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.158467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.119893 restraints weight = 30993.076| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.06 r_work: 0.3230 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9510 Z= 0.150 Angle : 0.498 7.911 12954 Z= 0.254 Chirality : 0.034 0.277 1559 Planarity : 0.003 0.039 1478 Dihedral : 10.825 120.139 2599 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.41 % Allowed : 12.12 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.31 (0.26), residues: 1075 helix: 2.39 (0.18), residues: 773 sheet: -3.61 (1.12), residues: 14 loop : -0.60 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1364 TYR 0.016 0.001 TYR A 206 PHE 0.013 0.001 PHE A1753 TRP 0.011 0.001 TRP A1423 HIS 0.008 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9501) covalent geometry : angle 0.48486 (12931) SS BOND : bond 0.00379 ( 4) SS BOND : angle 0.86254 ( 8) hydrogen bonds : bond 0.03475 ( 609) hydrogen bonds : angle 3.67696 ( 1734) link_BETA1-4 : bond 0.00195 ( 2) link_BETA1-4 : angle 1.26761 ( 6) link_NAG-ASN : bond 0.00924 ( 3) link_NAG-ASN : angle 4.12448 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 127 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue SER 235 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue SER 355 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue THR 428 is missing expected H atoms. Skipping. Residue MET 726 is missing expected H atoms. Skipping. Residue VAL 752 is missing expected H atoms. Skipping. Residue LEU 755 is missing expected H atoms. Skipping. Residue MET 765 is missing expected H atoms. Skipping. Residue THR 766 is missing expected H atoms. Skipping. Residue ILE 769 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue TYR 775 is missing expected H atoms. Skipping. Residue TYR 776 is missing expected H atoms. Skipping. Residue TYR 777 is missing expected H atoms. Skipping. Residue ILE 788 is missing expected H atoms. Skipping. Residue ILE 791 is missing expected H atoms. Skipping. Residue LEU 792 is missing expected H atoms. Skipping. Residue SER 793 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue MET 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue LEU 808 is missing expected H atoms. Skipping. Residue SER 876 is missing expected H atoms. Skipping. Residue LEU 878 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue LYS 1302 is missing expected H atoms. Skipping. Residue MET 1499 is missing expected H atoms. Skipping. Residue LYS 1506 is missing expected H atoms. Skipping. Residue LYS 1507 is missing expected H atoms. Skipping. Residue ILE 1526 is missing expected H atoms. Skipping. Residue LYS 1529 is missing expected H atoms. Skipping. Residue TYR 1587 is missing expected H atoms. Skipping. Residue TYR 1588 is missing expected H atoms. Skipping. Residue THR 1590 is missing expected H atoms. Skipping. Residue ILE 1613 is missing expected H atoms. Skipping. Residue VAL 1626 is missing expected H atoms. Skipping. Residue ILE 1627 is missing expected H atoms. Skipping. Residue SER 1737 is missing expected H atoms. Skipping. Residue SER 1740 is missing expected H atoms. Skipping. Residue TYR 1769 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 163 average time/residue: 0.1790 time to fit residues: 42.8090 Evaluate side-chains 167 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 1206 HIS Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1343 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 86 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS ** A 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1695 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.157380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.118780 restraints weight = 31340.693| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.07 r_work: 0.3214 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9510 Z= 0.176 Angle : 0.527 9.070 12954 Z= 0.267 Chirality : 0.035 0.279 1559 Planarity : 0.003 0.041 1478 Dihedral : 11.026 125.769 2599 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.53 % Allowed : 11.88 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.21 (0.26), residues: 1075 helix: 2.32 (0.18), residues: 772 sheet: -3.60 (1.13), residues: 14 loop : -0.65 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1364 TYR 0.020 0.001 TYR A 206 PHE 0.013 0.001 PHE A1753 TRP 0.012 0.001 TRP A1423 HIS 0.009 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9501) covalent geometry : angle 0.51465 (12931) SS BOND : bond 0.00405 ( 4) SS BOND : angle 0.92334 ( 8) hydrogen bonds : bond 0.03612 ( 609) hydrogen bonds : angle 3.73209 ( 1734) link_BETA1-4 : bond 0.00142 ( 2) link_BETA1-4 : angle 1.25679 ( 6) link_NAG-ASN : bond 0.00898 ( 3) link_NAG-ASN : angle 4.14110 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4798.96 seconds wall clock time: 82 minutes 12.43 seconds (4932.43 seconds total)