Starting phenix.real_space_refine on Tue Nov 19 10:53:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6p_28887/11_2024/8f6p_28887_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6p_28887/11_2024/8f6p_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6p_28887/11_2024/8f6p_28887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6p_28887/11_2024/8f6p_28887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6p_28887/11_2024/8f6p_28887_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f6p_28887/11_2024/8f6p_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-5513/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: 9.97, per 1000 atoms: 0.57 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: 6.26 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: 1.28 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: 6.53 Time building geometry restraints manager: 6.37 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: 3.140 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: 0.320 Extract box with map and model: 0.750 Check model and map are aligned: 0.170 Set scattering table: 0.320 Process input model: 41.300 Find NCS groups from input model: 0.150 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.080 ------------------------------------------------------------------------------- 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 9501 Z= 0.614 Angle : 1.334 26.411 12931 Z= 0.492 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 *********************** 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 : 1.424 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: 0.4909 time to fit residues: 129.4697 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 : 1.365 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 9501 Z= 0.165 Angle : 0.530 8.030 12931 Z= 0.263 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 *********************** 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 : 1.382 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 outliers start: 6 outliers final: 6 residues processed: 173 average time/residue: 0.4060 time to fit residues: 103.9048 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 : 1.404 ------------------------------------------------------------------------------- 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 55 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9501 Z= 0.307 Angle : 0.577 10.172 12931 Z= 0.291 Chirality : 0.037 0.304 1559 Planarity : 0.004 0.041 1478 Dihedral : 15.143 167.142 2601 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.94 % Allowed : 9.18 % Favored : 89.88 % 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: 1.95 (0.26), residues: 1075 helix: 2.07 (0.18), residues: 770 sheet: -3.43 (1.20), residues: 14 loop : -0.55 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1423 HIS 0.003 0.001 HIS A 152 PHE 0.015 0.002 PHE A1754 TYR 0.020 0.002 TYR A 379 ARG 0.004 0.000 ARG A1364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 127 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue SER 235 is missing expected H atoms. Skipping. Residue LYS 249 is missing expected H atoms. Skipping. Residue LYS 250 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 291 is missing expected H atoms. Skipping. Residue LEU 300 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue SER 355 is missing expected H atoms. Skipping. Residue SER 358 is missing expected H atoms. Skipping. Residue ILE 425 is missing expected H atoms. Skipping. Residue THR 428 is missing expected H atoms. Skipping. Residue MET 726 is missing expected H atoms. Skipping. Residue VAL 752 is missing expected H atoms. Skipping. Residue LEU 755 is missing expected H atoms. Skipping. Residue MET 765 is missing expected H atoms. Skipping. Residue THR 766 is missing expected H atoms. Skipping. Residue ILE 769 is missing expected H atoms. Skipping. Residue ILE 770 is missing expected H atoms. Skipping. Residue LEU 772 is missing expected H atoms. Skipping. Residue TYR 775 is missing expected H atoms. Skipping. Residue TYR 776 is missing expected H atoms. Skipping. Residue TYR 777 is missing expected H atoms. Skipping. Residue ILE 788 is missing expected H atoms. Skipping. Residue ILE 791 is missing expected H atoms. Skipping. Residue LEU 792 is missing expected H atoms. Skipping. Residue SER 793 is missing expected H atoms. Skipping. Residue LEU 794 is missing expected H atoms. Skipping. Residue MET 795 is missing expected H atoms. Skipping. Residue LEU 797 is missing expected H atoms. Skipping. Residue LEU 808 is missing expected H atoms. Skipping. Residue SER 876 is missing expected H atoms. Skipping. Residue LEU 878 is missing expected H atoms. Skipping. Residue LYS 1198 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue LYS 1302 is missing expected H atoms. Skipping. Residue MET 1499 is missing expected H atoms. Skipping. Residue LYS 1506 is missing expected H atoms. Skipping. Residue LYS 1507 is missing expected H atoms. Skipping. Residue ILE 1526 is missing expected H atoms. Skipping. Residue LYS 1529 is missing expected H atoms. Skipping. Residue TYR 1587 is missing expected H atoms. Skipping. Residue TYR 1588 is missing expected H atoms. Skipping. Residue THR 1590 is missing expected H atoms. Skipping. Residue ILE 1613 is missing expected H atoms. Skipping. Residue VAL 1626 is missing expected H atoms. Skipping. Residue ILE 1627 is missing expected H atoms. Skipping. Residue SER 1737 is missing expected H atoms. Skipping. Residue SER 1740 is missing expected H atoms. Skipping. Residue TYR 1769 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 1.025 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: 0.8255 (tmmt) cc_final: 0.8020 (tptm) REVERT: A 1248 PHE cc_start: 0.8134 (m-80) cc_final: 0.7822 (m-80) REVERT: A 1364 ARG cc_start: 0.6896 (OUTLIER) cc_final: 0.6676 (mtt90) outliers start: 8 outliers final: 7 residues processed: 167 average time/residue: 0.4597 time to fit residues: 111.3730 Evaluate side-chains 163 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 816 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 Chi-restraints excluded: chain A residue 1608 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 66 optimal weight: 0.1980 chunk 99 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9501 Z= 0.154 Angle : 0.471 5.585 12931 Z= 0.242 Chirality : 0.034 0.270 1559 Planarity : 0.003 0.039 1478 Dihedral : 13.603 176.174 2599 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.18 % Allowed : 10.35 % 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: 2.26 (0.26), residues: 1075 helix: 2.29 (0.18), residues: 765 sheet: -3.59 (1.15), residues: 14 loop : -0.35 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1423 HIS 0.002 0.000 HIS A 152 PHE 0.014 0.001 PHE A1753 TYR 0.014 0.001 TYR A 379 ARG 0.001 0.000 ARG A1314 *********************** 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 172 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 1.313 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: 0.8167 (tmmt) cc_final: 0.7915 (tptm) outliers start: 10 outliers final: 8 residues processed: 165 average time/residue: 0.4224 time to fit residues: 102.1409 Evaluate side-chains 165 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 1206 HIS Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1343 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9501 Z= 0.237 Angle : 0.511 7.078 12931 Z= 0.260 Chirality : 0.035 0.276 1559 Planarity : 0.003 0.040 1478 Dihedral : 12.735 129.287 2599 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.06 % Allowed : 11.18 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.15 (0.26), residues: 1075 helix: 2.23 (0.18), residues: 771 sheet: -3.48 (1.19), residues: 14 loop : -0.52 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 0.005 0.000 ARG A 815 *********************** 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 165 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 160 average time/residue: 0.4447 time to fit residues: 104.5456 Evaluate side-chains 165 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 1206 HIS Chi-restraints excluded: chain A residue 1219 LEU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1343 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9501 Z= 0.198 Angle : 0.478 5.698 12931 Z= 0.248 Chirality : 0.034 0.271 1559 Planarity : 0.003 0.039 1478 Dihedral : 11.796 123.383 2599 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.88 % Allowed : 11.06 % Favored : 87.06 % 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: 2.21 (0.26), residues: 1075 helix: 2.28 (0.18), residues: 771 sheet: -3.41 (1.22), residues: 14 loop : -0.52 (0.37), residues: 290 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 0.016 0.001 TYR A 379 ARG 0.003 0.000 ARG A 815 *********************** 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 172 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 1.296 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: 0.6870 (OUTLIER) cc_final: 0.6652 (mtt90) outliers start: 16 outliers final: 11 residues processed: 165 average time/residue: 0.4183 time to fit residues: 101.2064 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 : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU 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 11 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9501 Z= 0.243 Angle : 0.495 6.295 12931 Z= 0.257 Chirality : 0.035 0.274 1559 Planarity : 0.003 0.040 1478 Dihedral : 11.581 125.433 2599 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.53 % Allowed : 11.88 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.12 (0.26), residues: 1075 helix: 2.24 (0.18), residues: 773 sheet: -3.28 (1.29), residues: 14 loop : -0.68 (0.36), residues: 288 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 0.003 0.000 ARG A 815 *********************** 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 169 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 1.475 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 1364 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6634 (mtt90) outliers start: 13 outliers final: 10 residues processed: 163 average time/residue: 0.4109 time to fit residues: 97.3936 Evaluate side-chains 168 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU 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 62 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.3980 chunk 66 optimal weight: 0.4980 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9501 Z= 0.213 Angle : 0.480 6.452 12931 Z= 0.249 Chirality : 0.034 0.270 1559 Planarity : 0.003 0.040 1478 Dihedral : 11.272 122.668 2599 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.41 % Allowed : 12.47 % 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: 2.17 (0.26), residues: 1075 helix: 2.28 (0.18), residues: 773 sheet: -3.44 (1.22), residues: 14 loop : -0.67 (0.36), residues: 288 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 0.017 0.001 TYR A 379 ARG 0.002 0.000 ARG A1364 *********************** 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 171 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 1.366 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: 0.6948 (OUTLIER) cc_final: 0.6718 (mtt90) outliers start: 12 outliers final: 11 residues processed: 165 average time/residue: 0.4027 time to fit residues: 96.7716 Evaluate side-chains 170 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU 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 97 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9501 Z= 0.210 Angle : 0.482 6.460 12931 Z= 0.250 Chirality : 0.034 0.270 1559 Planarity : 0.003 0.040 1478 Dihedral : 11.144 122.218 2599 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.53 % Allowed : 12.71 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.30 (0.18), residues: 773 sheet: -3.40 (1.24), residues: 14 loop : -0.66 (0.36), residues: 288 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 0.016 0.001 TYR A 379 ARG 0.002 0.000 ARG A1364 *********************** 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 169 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 1.349 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: 0.6956 (OUTLIER) cc_final: 0.6727 (mtt90) outliers start: 13 outliers final: 11 residues processed: 162 average time/residue: 0.4109 time to fit residues: 97.3249 Evaluate side-chains 168 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU 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 49 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9501 Z= 0.213 Angle : 0.481 6.042 12931 Z= 0.249 Chirality : 0.034 0.271 1559 Planarity : 0.003 0.040 1478 Dihedral : 11.056 121.270 2599 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.41 % Allowed : 12.71 % Favored : 85.88 % 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: 2.31 (0.18), residues: 772 sheet: -3.39 (1.24), residues: 14 loop : -0.67 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1423 HIS 0.002 0.001 HIS A 152 PHE 0.014 0.001 PHE A1753 TYR 0.019 0.001 TYR A 206 ARG 0.002 0.000 ARG A1364 ********************** 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 171 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 1.465 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: 0.6917 (OUTLIER) cc_final: 0.6696 (mtt90) outliers start: 12 outliers final: 11 residues processed: 165 average time/residue: 0.4114 time to fit residues: 99.4197 Evaluate side-chains 169 residues out of total 959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU 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 79 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3847 r_free = 0.3847 target = 0.159159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120809 restraints weight = 31231.394| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.07 r_work: 0.3240 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9501 Z= 0.159 Angle : 0.466 6.407 12931 Z= 0.240 Chirality : 0.033 0.258 1559 Planarity : 0.003 0.039 1478 Dihedral : 10.729 111.417 2599 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.18 % Allowed : 13.88 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.29 (0.26), residues: 1075 helix: 2.37 (0.18), residues: 773 sheet: -3.46 (1.19), residues: 14 loop : -0.61 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1442 HIS 0.001 0.000 HIS A 152 PHE 0.015 0.001 PHE A1753 TYR 0.016 0.001 TYR A 206 ARG 0.001 0.000 ARG A1314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4007.04 seconds wall clock time: 113 minutes 13.21 seconds (6793.21 seconds total)