Starting phenix.real_space_refine on Mon Jun 16 23:06:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6p_28887/06_2025/8f6p_28887_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6p_28887/06_2025/8f6p_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8f6p_28887/06_2025/8f6p_28887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6p_28887/06_2025/8f6p_28887.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6p_28887/06_2025/8f6p_28887_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6p_28887/06_2025/8f6p_28887_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 9, 'GLU:plan': 13, 'ARG:plan': 8} 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: {'Y01:plan-2': 1, 'Y01:plan-1': 1, '6OU:plan-1': 2} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 9.21, per 1000 atoms: 0.53 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: 5.15 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.57 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: 6.94 Time building geometry restraints manager: 6.02 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.310 Extract box with map and model: 0.680 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 41.140 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.930 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.022 0.001 TRP A1423 HIS 0.003 0.001 HIS A 152 PHE 0.015 0.001 PHE A1753 TYR 0.017 0.001 TYR A 379 ARG 0.002 0.000 ARG A1305 Details of bonding type rmsd link_NAG-ASN : bond 0.00943 ( 3) link_NAG-ASN : angle 4.49106 ( 9) link_BETA1-4 : bond 0.01401 ( 2) link_BETA1-4 : angle 5.95753 ( 6) hydrogen bonds : bond 0.11062 ( 609) hydrogen bonds : angle 5.02745 ( 1734) SS BOND : bond 0.00335 ( 4) SS BOND : angle 1.36365 ( 8) covalent geometry : bond 0.01038 ( 9501) covalent geometry : angle 1.33362 (12931) *********************** 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 : 1.303 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: 0.3793 time to fit residues: 98.7774 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 : 1.319 ------------------------------------------------------------------------------- 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 92 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 0.0980 chunk 44 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.158669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.122460 restraints weight = 30788.875| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.97 r_work: 0.3274 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9510 Z= 0.120 Angle : 0.549 8.051 12954 Z= 0.267 Chirality : 0.036 0.308 1559 Planarity : 0.003 0.038 1478 Dihedral : 16.817 157.905 2601 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.71 % Allowed : 6.71 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.26), residues: 1075 helix: 2.26 (0.19), residues: 755 sheet: -3.68 (1.12), residues: 14 loop : -0.33 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1423 HIS 0.002 0.001 HIS A 152 PHE 0.016 0.001 PHE A1455 TYR 0.014 0.001 TYR A 379 ARG 0.003 0.000 ARG A1434 Details of bonding type rmsd link_NAG-ASN : bond 0.00967 ( 3) link_NAG-ASN : angle 5.20595 ( 9) link_BETA1-4 : bond 0.00323 ( 2) link_BETA1-4 : angle 2.32666 ( 6) hydrogen bonds : bond 0.03959 ( 609) hydrogen bonds : angle 4.01384 ( 1734) SS BOND : bond 0.00250 ( 4) SS BOND : angle 0.83030 ( 8) covalent geometry : bond 0.00255 ( 9501) covalent geometry : angle 0.52977 (12931) *********************** 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 177 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 171 time to evaluate : 1.272 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: 0.8814 (m-80) cc_final: 0.8527 (m-80) REVERT: A 1572 ILE cc_start: 0.8246 (mt) cc_final: 0.8034 (mt) outliers start: 6 outliers final: 6 residues processed: 173 average time/residue: 0.4464 time to fit residues: 114.2015 Evaluate side-chains 169 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 163 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 52 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.158484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.120038 restraints weight = 31087.184| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.06 r_work: 0.3230 rms_B_bonded: 2.79 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: 0.7879 moved from start: 0.1038 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= 0.163 Angle : 0.550 10.085 12954 Z= 0.272 Chirality : 0.035 0.295 1559 Planarity : 0.003 0.040 1478 Dihedral : 14.857 165.286 2601 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.71 % Allowed : 8.59 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.26), residues: 1075 helix: 2.21 (0.18), residues: 765 sheet: -3.58 (1.15), residues: 14 loop : -0.36 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1423 HIS 0.002 0.001 HIS A 152 PHE 0.014 0.001 PHE A1753 TYR 0.018 0.001 TYR A 379 ARG 0.003 0.000 ARG A1364 Details of bonding type rmsd link_NAG-ASN : bond 0.01055 ( 3) link_NAG-ASN : angle 4.80494 ( 9) link_BETA1-4 : bond 0.00124 ( 2) link_BETA1-4 : angle 1.80450 ( 6) hydrogen bonds : bond 0.03919 ( 609) hydrogen bonds : angle 3.92907 ( 1734) SS BOND : bond 0.00350 ( 4) SS BOND : angle 0.87357 ( 8) covalent geometry : bond 0.00368 ( 9501) covalent geometry : angle 0.53358 (12931) *********************** 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 171 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 165 time to evaluate : 1.461 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 159 LYS cc_start: 0.8483 (tmmt) cc_final: 0.8067 (tptm) REVERT: A 1248 PHE cc_start: 0.7932 (m-80) cc_final: 0.7658 (m-80) REVERT: A 1411 TYR cc_start: 0.8919 (m-80) cc_final: 0.8562 (m-80) outliers start: 6 outliers final: 6 residues processed: 167 average time/residue: 0.4446 time to fit residues: 108.3313 Evaluate side-chains 164 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 158 time to evaluate : 1.384 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 9 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.159309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121070 restraints weight = 31045.456| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.06 r_work: 0.3241 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1218 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= 0.126 Angle : 0.497 8.013 12954 Z= 0.250 Chirality : 0.034 0.268 1559 Planarity : 0.003 0.039 1478 Dihedral : 13.792 179.713 2601 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.82 % Allowed : 10.00 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.26), residues: 1075 helix: 2.29 (0.18), residues: 765 sheet: -3.55 (1.17), residues: 14 loop : -0.34 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1423 HIS 0.002 0.001 HIS A 152 PHE 0.014 0.001 PHE A1753 TYR 0.015 0.001 TYR A 379 ARG 0.003 0.000 ARG A 815 Details of bonding type rmsd link_NAG-ASN : bond 0.01019 ( 3) link_NAG-ASN : angle 4.53524 ( 9) link_BETA1-4 : bond 0.00159 ( 2) link_BETA1-4 : angle 1.52554 ( 6) hydrogen bonds : bond 0.03627 ( 609) hydrogen bonds : angle 3.79556 ( 1734) SS BOND : bond 0.00334 ( 4) SS BOND : angle 0.78523 ( 8) covalent geometry : bond 0.00279 ( 9501) covalent geometry : angle 0.48087 (12931) *********************** 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 168 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 161 time to evaluate : 1.211 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 159 LYS cc_start: 0.8456 (tmmt) cc_final: 0.8000 (tptm) REVERT: A 1248 PHE cc_start: 0.7917 (m-80) cc_final: 0.7628 (m-80) REVERT: A 1411 TYR cc_start: 0.8931 (m-80) cc_final: 0.8702 (m-80) outliers start: 7 outliers final: 6 residues processed: 163 average time/residue: 0.4434 time to fit residues: 106.2660 Evaluate side-chains 164 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 158 time to evaluate : 1.551 ------------------------------------------------------------------------------- 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 96 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 66 optimal weight: 0.0470 chunk 77 optimal weight: 1.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.156075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119631 restraints weight = 31179.597| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.97 r_work: 0.3237 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1330 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= 0.150 Angle : 0.513 8.152 12954 Z= 0.258 Chirality : 0.035 0.273 1559 Planarity : 0.003 0.040 1478 Dihedral : 12.720 142.543 2599 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.53 % Allowed : 10.00 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.26), residues: 1075 helix: 2.29 (0.18), residues: 766 sheet: -3.41 (1.23), residues: 14 loop : -0.36 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1423 HIS 0.002 0.001 HIS A 883 PHE 0.014 0.001 PHE A1753 TYR 0.017 0.001 TYR A 379 ARG 0.004 0.000 ARG A 815 Details of bonding type rmsd link_NAG-ASN : bond 0.00958 ( 3) link_NAG-ASN : angle 4.45597 ( 9) link_BETA1-4 : bond 0.00242 ( 2) link_BETA1-4 : angle 1.32433 ( 6) hydrogen bonds : bond 0.03619 ( 609) hydrogen bonds : angle 3.74924 ( 1734) SS BOND : bond 0.00356 ( 4) SS BOND : angle 0.83138 ( 8) covalent geometry : bond 0.00341 ( 9501) covalent geometry : angle 0.49908 (12931) *********************** 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 : 2.061 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: 0.7384 (OUTLIER) cc_final: 0.7140 (mtt90) REVERT: A 1411 TYR cc_start: 0.8960 (m-80) cc_final: 0.8638 (m-80) outliers start: 13 outliers final: 11 residues processed: 164 average time/residue: 0.5622 time to fit residues: 138.8196 Evaluate side-chains 167 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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 38 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 36 optimal weight: 8.9990 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 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 = 0.3807 r_free = 0.3807 target = 0.155486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.119068 restraints weight = 31095.089| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.96 r_work: 0.3230 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9510 Z= 0.161 Angle : 0.510 8.068 12954 Z= 0.259 Chirality : 0.035 0.272 1559 Planarity : 0.003 0.040 1478 Dihedral : 11.964 125.808 2599 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.65 % Allowed : 11.06 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.26), residues: 1075 helix: 2.27 (0.18), residues: 771 sheet: -3.34 (1.26), residues: 14 loop : -0.52 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1423 HIS 0.002 0.001 HIS A 152 PHE 0.014 0.001 PHE A1753 TYR 0.017 0.001 TYR A 379 ARG 0.002 0.000 ARG A1364 Details of bonding type rmsd link_NAG-ASN : bond 0.00930 ( 3) link_NAG-ASN : angle 4.42256 ( 9) link_BETA1-4 : bond 0.00187 ( 2) link_BETA1-4 : angle 1.33986 ( 6) hydrogen bonds : bond 0.03638 ( 609) hydrogen bonds : angle 3.75233 ( 1734) SS BOND : bond 0.00374 ( 4) SS BOND : angle 0.85525 ( 8) covalent geometry : bond 0.00367 ( 9501) covalent geometry : angle 0.49585 (12931) *********************** 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: 14 poor density : 157 time to evaluate : 1.258 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: 0.7396 (OUTLIER) cc_final: 0.7143 (mtt90) REVERT: A 1411 TYR cc_start: 0.8967 (m-80) cc_final: 0.8664 (m-80) outliers start: 14 outliers final: 12 residues processed: 165 average time/residue: 0.4387 time to fit residues: 108.2661 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 : 1.205 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 31 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.155593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.116908 restraints weight = 31240.647| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.05 r_work: 0.3189 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9510 Z= 0.217 Angle : 0.564 8.205 12954 Z= 0.288 Chirality : 0.037 0.285 1559 Planarity : 0.004 0.041 1478 Dihedral : 12.122 129.372 2599 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.65 % Allowed : 12.00 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.26), residues: 1075 helix: 2.12 (0.18), residues: 771 sheet: -3.18 (1.36), residues: 14 loop : -0.63 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1423 HIS 0.003 0.001 HIS A 883 PHE 0.015 0.002 PHE A1404 TYR 0.020 0.002 TYR A 379 ARG 0.004 0.000 ARG A1364 Details of bonding type rmsd link_NAG-ASN : bond 0.00862 ( 3) link_NAG-ASN : angle 4.53532 ( 9) link_BETA1-4 : bond 0.00219 ( 2) link_BETA1-4 : angle 1.30130 ( 6) hydrogen bonds : bond 0.03968 ( 609) hydrogen bonds : angle 3.88456 ( 1734) SS BOND : bond 0.00458 ( 4) SS BOND : angle 1.03670 ( 8) covalent geometry : bond 0.00503 ( 9501) covalent geometry : angle 0.55012 (12931) *********************** 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 167 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1364 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.7099 (mtt90) REVERT: A 1411 TYR cc_start: 0.9016 (m-80) cc_final: 0.8547 (m-80) outliers start: 14 outliers final: 11 residues processed: 162 average time/residue: 0.3768 time to fit residues: 90.1772 Evaluate side-chains 164 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 1364 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.157903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.119494 restraints weight = 31120.995| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.06 r_work: 0.3224 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9510 Z= 0.131 Angle : 0.492 7.820 12954 Z= 0.251 Chirality : 0.034 0.266 1559 Planarity : 0.003 0.040 1478 Dihedral : 11.471 120.310 2599 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.88 % Allowed : 12.00 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.26), residues: 1075 helix: 2.22 (0.18), residues: 773 sheet: -3.31 (1.31), residues: 14 loop : -0.70 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1442 HIS 0.002 0.001 HIS A 152 PHE 0.015 0.001 PHE A1753 TYR 0.016 0.001 TYR A 379 ARG 0.001 0.000 ARG A1364 Details of bonding type rmsd link_NAG-ASN : bond 0.00971 ( 3) link_NAG-ASN : angle 4.26789 ( 9) link_BETA1-4 : bond 0.00166 ( 2) link_BETA1-4 : angle 1.27439 ( 6) hydrogen bonds : bond 0.03589 ( 609) hydrogen bonds : angle 3.73902 ( 1734) SS BOND : bond 0.00376 ( 4) SS BOND : angle 0.85085 ( 8) covalent geometry : bond 0.00292 ( 9501) covalent geometry : angle 0.47771 (12931) *********************** 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 173 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1364 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.7044 (mtt90) REVERT: A 1411 TYR cc_start: 0.9004 (m-80) cc_final: 0.8693 (m-80) outliers start: 16 outliers final: 12 residues processed: 166 average time/residue: 0.3820 time to fit residues: 93.4427 Evaluate side-chains 170 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 1364 ARG Chi-restraints excluded: chain A residue 1708 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 99 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.157249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.118625 restraints weight = 31339.680| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.07 r_work: 0.3213 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9510 Z= 0.158 Angle : 0.514 7.838 12954 Z= 0.261 Chirality : 0.035 0.273 1559 Planarity : 0.003 0.040 1478 Dihedral : 11.415 124.682 2599 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.53 % Allowed : 12.35 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.26), residues: 1075 helix: 2.21 (0.18), residues: 772 sheet: -3.28 (1.31), residues: 14 loop : -0.68 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1423 HIS 0.002 0.001 HIS A 152 PHE 0.014 0.001 PHE A1753 TYR 0.018 0.001 TYR A 379 ARG 0.002 0.000 ARG A1364 Details of bonding type rmsd link_NAG-ASN : bond 0.00931 ( 3) link_NAG-ASN : angle 4.25956 ( 9) link_BETA1-4 : bond 0.00172 ( 2) link_BETA1-4 : angle 1.26687 ( 6) hydrogen bonds : bond 0.03648 ( 609) hydrogen bonds : angle 3.77222 ( 1734) SS BOND : bond 0.00408 ( 4) SS BOND : angle 0.90958 ( 8) covalent geometry : bond 0.00362 ( 9501) covalent geometry : angle 0.50058 (12931) *********************** 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 168 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1364 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.7090 (mtt90) REVERT: A 1411 TYR cc_start: 0.9027 (m-80) cc_final: 0.8672 (m-80) outliers start: 13 outliers final: 12 residues processed: 161 average time/residue: 0.3924 time to fit residues: 93.4267 Evaluate side-chains 167 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 1.333 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 1364 ARG Chi-restraints excluded: chain A residue 1708 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 65 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.158139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119772 restraints weight = 31225.087| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.06 r_work: 0.3208 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9510 Z= 0.126 Angle : 0.488 7.720 12954 Z= 0.248 Chirality : 0.034 0.263 1559 Planarity : 0.003 0.039 1478 Dihedral : 11.067 117.191 2599 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.53 % Allowed : 12.12 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.26), residues: 1075 helix: 2.29 (0.18), residues: 772 sheet: -3.44 (1.23), residues: 14 loop : -0.65 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1442 HIS 0.002 0.001 HIS A 152 PHE 0.015 0.001 PHE A1753 TYR 0.016 0.001 TYR A 379 ARG 0.001 0.000 ARG A1314 Details of bonding type rmsd link_NAG-ASN : bond 0.00972 ( 3) link_NAG-ASN : angle 4.14235 ( 9) link_BETA1-4 : bond 0.00155 ( 2) link_BETA1-4 : angle 1.25959 ( 6) hydrogen bonds : bond 0.03490 ( 609) hydrogen bonds : angle 3.70524 ( 1734) SS BOND : bond 0.00370 ( 4) SS BOND : angle 0.83800 ( 8) covalent geometry : bond 0.00283 ( 9501) covalent geometry : angle 0.47475 (12931) ********************** 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 172 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1364 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.7046 (mtt90) REVERT: A 1411 TYR cc_start: 0.9008 (m-80) cc_final: 0.8647 (m-80) outliers start: 13 outliers final: 12 residues processed: 165 average time/residue: 0.3865 time to fit residues: 94.0826 Evaluate side-chains 171 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 1.385 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 1364 ARG Chi-restraints excluded: chain A residue 1708 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 95 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.158894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.120638 restraints weight = 31191.112| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.06 r_work: 0.3241 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1698 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= 0.112 Angle : 0.480 7.655 12954 Z= 0.242 Chirality : 0.033 0.259 1559 Planarity : 0.003 0.039 1478 Dihedral : 10.719 108.172 2599 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.29 % Allowed : 12.71 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.26), residues: 1075 helix: 2.37 (0.18), residues: 773 sheet: -3.44 (1.19), residues: 14 loop : -0.60 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1442 HIS 0.002 0.000 HIS A 152 PHE 0.014 0.001 PHE A1753 TYR 0.021 0.001 TYR A 206 ARG 0.001 0.000 ARG A1314 Details of bonding type rmsd link_NAG-ASN : bond 0.00989 ( 3) link_NAG-ASN : angle 4.04375 ( 9) link_BETA1-4 : bond 0.00122 ( 2) link_BETA1-4 : angle 1.22051 ( 6) hydrogen bonds : bond 0.03380 ( 609) hydrogen bonds : angle 3.65320 ( 1734) SS BOND : bond 0.00279 ( 4) SS BOND : angle 0.72693 ( 8) covalent geometry : bond 0.00249 ( 9501) covalent geometry : angle 0.46714 (12931) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10184.13 seconds wall clock time: 178 minutes 44.97 seconds (10724.97 seconds total)