Starting phenix.real_space_refine on Fri Sep 11 16:21:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uz0_20949/09_2026/6uz0_20949.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uz0_20949/09_2026/6uz0_20949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uz0_20949/09_2026/6uz0_20949.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uz0_20949/09_2026/6uz0_20949.map" model { file = "/net/cci-nas-00/data/ceres_data/6uz0_20949/09_2026/6uz0_20949.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uz0_20949/09_2026/6uz0_20949.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6uz0_20949/09_2026/6uz0_20949.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uz0_20949/09_2026/6uz0_20949.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.010 sd= 1.805 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 5 5.49 5 S 68 5.16 5 C 6383 2.51 5 N 1440 2.21 5 O 1655 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9557 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1138, 8970 Classifications: {'peptide': 1138} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 30, 'TRANS': 1105} Chain breaks: 5 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 8, 'PHE:plan': 2, 'TYR:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 106 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 492 Unusual residues: {'6OU': 11, '9Z9': 5, 'K4D': 1, 'NAG': 2} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 232 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'6OU:plan-1': 9, '6OU:plan-3': 1, '6OU:plan-2': 2} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 1.61, per 1000 atoms: 0.17 Number of scatterers: 9557 At special positions: 0 Unit cell: (136.224, 126.72, 108.768, 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 68 16.00 P 5 15.00 F 6 9.00 O 1655 8.00 N 1440 7.00 C 6383 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 336 " distance=2.63 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 342 " distance=2.02 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 918 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A3003 " - " ASN A 319 " " NAG A3009 " - " ASN A 284 " " NAG B 1 " - " ASN A1382 " " NAG C 1 " - " ASN A 329 " " NAG D 1 " - " ASN A1390 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 304.6 milliseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 1 sheets defined 79.3% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 119 through 131 Processing helix chain 'A' and resid 131 through 150 removed outlier: 4.177A pdb=" N SER A 135 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 181 removed outlier: 4.254A pdb=" N VAL A 161 " --> pdb=" O TRP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 192 removed outlier: 3.875A pdb=" N ASP A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 211 removed outlier: 3.769A pdb=" N TRP A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP A 198 " --> pdb=" O TRP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.672A pdb=" N ARG A 220 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 221 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG A 223 " --> pdb=" O ARG A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 236 through 251 removed outlier: 3.808A pdb=" N GLN A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 274 Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.514A pdb=" N HIS A 279 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 removed outlier: 3.954A pdb=" N ASN A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 372 removed outlier: 3.832A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 386 removed outlier: 4.084A 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 401 Processing helix chain 'A' and resid 401 through 430 Processing helix chain 'A' and resid 700 through 715 Processing helix chain 'A' and resid 720 through 737 Processing helix chain 'A' and resid 743 through 770 Processing helix chain 'A' and resid 773 through 780 removed outlier: 3.877A pdb=" N TYR A 777 " --> pdb=" O ASP A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 798 Processing helix chain 'A' and resid 806 through 822 removed outlier: 4.365A pdb=" N ARG A 809 " --> pdb=" O SER A 806 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE A 811 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 813 " --> pdb=" O SER A 810 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 819 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 821 " --> pdb=" O LYS A 818 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER A 822 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 837 removed outlier: 3.841A pdb=" N VAL A 837 " --> pdb=" O ILE A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 869 removed outlier: 6.327A pdb=" N LYS A 864 " --> pdb=" O GLN A 860 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ASN A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 873 Processing helix chain 'A' and resid 887 through 900 Processing helix chain 'A' and resid 902 through 913 removed outlier: 4.446A pdb=" N ASP A 908 " --> pdb=" O GLU A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 944 Processing helix chain 'A' and resid 1191 through 1205 Processing helix chain 'A' and resid 1206 through 1226 Processing helix chain 'A' and resid 1228 through 1232 removed outlier: 3.887A pdb=" N LEU A1231 " --> pdb=" O ASP A1228 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU A1232 " --> pdb=" O ILE A1229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1228 through 1232' Processing helix chain 'A' and resid 1234 through 1270 removed outlier: 4.270A pdb=" N VAL A1239 " --> pdb=" O LYS A1235 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N PHE A1265 " --> pdb=" O VAL A1261 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N LYS A1266 " --> pdb=" O ALA A1262 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS A1267 " --> pdb=" O TYR A1263 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A1269 " --> pdb=" O PHE A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1293 Processing helix chain 'A' and resid 1304 through 1313 Proline residue: A1312 - end of helix Processing helix chain 'A' and resid 1314 through 1319 removed outlier: 4.141A pdb=" N ARG A1318 " --> pdb=" O ARG A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1331 removed outlier: 3.534A pdb=" N VAL A1324 " --> pdb=" O GLU A1320 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1358 Processing helix chain 'A' and resid 1382 through 1390 removed outlier: 3.849A pdb=" N SER A1388 " --> pdb=" O SER A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1420 Processing helix chain 'A' and resid 1422 through 1431 removed outlier: 4.166A pdb=" N ILE A1426 " --> pdb=" O GLY A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1447 No H-bonds generated for 'chain 'A' and resid 1445 through 1447' Processing helix chain 'A' and resid 1448 through 1461 removed outlier: 3.770A pdb=" N PHE A1452 " --> pdb=" O MET A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1483 Processing helix chain 'A' and resid 1490 through 1503 Processing helix chain 'A' and resid 1517 through 1529 removed outlier: 3.683A pdb=" N LYS A1529 " --> pdb=" O ASP A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1549 removed outlier: 3.939A pdb=" N ASP A1533 " --> pdb=" O LYS A1529 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A1534 " --> pdb=" O GLN A1530 " (cutoff:3.500A) removed outlier: 3.692A 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 1586 through 1591 removed outlier: 4.788A pdb=" N ASN A1591 " --> pdb=" O TYR A1587 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1612 Processing helix chain 'A' and resid 1613 through 1618 removed outlier: 3.865A pdb=" N TYR A1617 " --> pdb=" O ILE A1613 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1630 removed outlier: 3.658A pdb=" N VAL A1626 " --> pdb=" O THR A1622 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE A1627 " --> pdb=" O LEU A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1631 through 1636 removed outlier: 4.143A pdb=" N ILE A1635 " --> pdb=" O ARG A1631 " (cutoff:3.500A) Processing helix chain 'A' and resid 1637 through 1640 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: 3.574A pdb=" N SER A1702 " --> pdb=" O THR A1698 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A1711 " --> pdb=" O PHE A1707 " (cutoff:3.500A) Processing helix chain 'A' and resid 1714 through 1724 Proline residue: A1721 - end of helix removed outlier: 4.010A pdb=" N ASN A1724 " --> pdb=" O SER A1720 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1780 Processing sheet with id=AA1, first strand: chain 'A' and resid 280 through 283 removed outlier: 3.884A pdb=" N LYS A 280 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 343 " --> pdb=" O LYS A 280 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1420 1.27 - 1.41: 2563 1.41 - 1.55: 5613 1.55 - 1.68: 67 1.68 - 1.82: 125 Bond restraints: 9788 Sorted by residual: bond pdb=" C06 9Z9 A3010 " pdb=" C07 9Z9 A3010 " ideal model delta sigma weight residual 1.520 1.135 0.385 2.00e-02 2.50e+03 3.70e+02 bond pdb=" C06 9Z9 A3014 " pdb=" C07 9Z9 A3014 " ideal model delta sigma weight residual 1.520 1.138 0.382 2.00e-02 2.50e+03 3.65e+02 bond pdb=" C06 9Z9 A3012 " pdb=" C07 9Z9 A3012 " ideal model delta sigma weight residual 1.520 1.140 0.380 2.00e-02 2.50e+03 3.60e+02 bond pdb=" C06 9Z9 A3011 " pdb=" C07 9Z9 A3011 " ideal model delta sigma weight residual 1.520 1.140 0.380 2.00e-02 2.50e+03 3.60e+02 bond pdb=" C06 9Z9 A3013 " pdb=" C07 9Z9 A3013 " ideal model delta sigma weight residual 1.520 1.145 0.375 2.00e-02 2.50e+03 3.52e+02 ... (remaining 9783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.64: 13211 7.64 - 15.27: 60 15.27 - 22.91: 4 22.91 - 30.55: 0 30.55 - 38.18: 1 Bond angle restraints: 13276 Sorted by residual: angle pdb=" N GLN A1368 " pdb=" CA GLN A1368 " pdb=" C GLN A1368 " ideal model delta sigma weight residual 111.28 123.02 -11.74 1.09e+00 8.42e-01 1.16e+02 angle pdb=" N TYR A 308 " pdb=" CA TYR A 308 " pdb=" C TYR A 308 " ideal model delta sigma weight residual 111.07 121.60 -10.53 1.07e+00 8.73e-01 9.68e+01 angle pdb=" N ARG A1318 " pdb=" CA ARG A1318 " pdb=" C ARG A1318 " ideal model delta sigma weight residual 111.36 121.68 -10.32 1.09e+00 8.42e-01 8.97e+01 angle pdb=" N ARG A1364 " pdb=" CA ARG A1364 " pdb=" C ARG A1364 " ideal model delta sigma weight residual 111.36 121.61 -10.25 1.09e+00 8.42e-01 8.85e+01 angle pdb=" C LEU A1373 " pdb=" N PRO A1374 " pdb=" CD PRO A1374 " ideal model delta sigma weight residual 125.00 86.82 38.18 4.10e+00 5.95e-02 8.67e+01 ... (remaining 13271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 5367 35.35 - 70.70: 176 70.70 - 106.05: 11 106.05 - 141.40: 6 141.40 - 176.75: 1 Dihedral angle restraints: 5561 sinusoidal: 2245 harmonic: 3316 Sorted by residual: dihedral pdb=" C TYR A 308 " pdb=" N TYR A 308 " pdb=" CA TYR A 308 " pdb=" CB TYR A 308 " ideal model delta harmonic sigma weight residual -122.60 -145.41 22.81 0 2.50e+00 1.60e-01 8.32e+01 dihedral pdb=" N TYR A 308 " pdb=" C TYR A 308 " pdb=" CA TYR A 308 " pdb=" CB TYR A 308 " ideal model delta harmonic sigma weight residual 122.80 144.35 -21.55 0 2.50e+00 1.60e-01 7.43e+01 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 93.00 152.64 -59.64 1 1.00e+01 1.00e-02 4.75e+01 ... (remaining 5558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.923: 1554 0.923 - 1.846: 5 1.846 - 2.769: 1 2.769 - 3.693: 0 3.693 - 4.616: 1 Chirality restraints: 1561 Sorted by residual: chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 2.22 -4.62 2.00e-02 2.50e+03 5.33e+04 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.81 0.41 2.00e-02 2.50e+03 4.13e+02 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 329 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.15 -2.25 2.00e-01 2.50e+01 1.26e+02 ... (remaining 1558 not shown) Planarity restraints: 1566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.340 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG D 2 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.063 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.519 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.195 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A3009 " -0.227 2.00e-02 2.50e+03 1.93e-01 4.66e+02 pdb=" C7 NAG A3009 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG A3009 " 0.036 2.00e-02 2.50e+03 pdb=" N2 NAG A3009 " 0.318 2.00e-02 2.50e+03 pdb=" O7 NAG A3009 " -0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.195 2.00e-02 2.50e+03 1.62e-01 3.28e+02 pdb=" C7 NAG C 1 " -0.053 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.141 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.264 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " -0.019 2.00e-02 2.50e+03 ... (remaining 1563 not shown) Histogram of nonbonded interaction distances: 0.58 - 1.45: 2 1.45 - 2.31: 31 2.31 - 3.17: 9076 3.17 - 4.04: 23201 4.04 - 4.90: 43299 Warning: very small nonbonded interaction distances. Nonbonded interactions: 75609 Sorted by model distance: nonbonded pdb=" OD1 ASN A 284 " pdb=" C8 NAG A3009 " model vdw 0.584 3.460 nonbonded pdb=" ND2 ASN A1724 " pdb=" SG CYS A1730 " model vdw 1.420 3.480 nonbonded pdb=" O ARG A1364 " pdb=" NE2 GLN A1439 " model vdw 1.461 3.120 nonbonded pdb=" CG ASN A 284 " pdb=" C8 NAG A3009 " model vdw 1.790 3.690 nonbonded pdb=" O ARG A 283 " pdb=" O ASN A 284 " model vdw 1.849 3.040 ... (remaining 75604 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 'D' } 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.950 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 0.023 0.603 9804 Z= 1.223 Angle : 1.557 43.125 13309 Z= 0.730 Chirality : 0.179 4.616 1561 Planarity : 0.013 0.294 1561 Dihedral : 17.788 176.748 3408 Min Nonbonded Distance : 0.584 Molprobity Statistics. All-atom Clashscore : 27.77 Ramachandran Plot: Outliers : 0.98 % Allowed : 7.55 % Favored : 91.47 % Rotamer: Outliers : 2.73 % Allowed : 9.75 % Favored : 87.53 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.23), residues: 1126 helix: -1.10 (0.17), residues: 794 sheet: None (None), residues: 0 loop : -3.10 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 123 TYR 0.031 0.002 TYR A 379 PHE 0.020 0.002 PHE A 394 TRP 0.021 0.002 TRP A1423 HIS 0.008 0.002 HIS A 883 Details of bonding type rmsd/Z covalent geometry : bond 0.02196 / 1.11 ( 9788) covalent geometry : angle 1.37752 / 0.68 (13276) SS BOND : bond 0.34831 / 18.33 ( 3) SS BOND : angle 14.06779 / 7.43 ( 6) hydrogen bonds : bond 0.12463 / 8.67 ( 625) hydrogen bonds : angle 6.22990 / 4.48 ( 1809) Misc. bond : bond 0.19233 / 9.69 ( 4) link_BETA1-4 : bond 0.03206 / 1.69 ( 4) link_BETA1-4 : angle 16.08000 / 8.29 ( 12) link_NAG-ASN : bond 0.14304 / 7.53 ( 5) link_NAG-ASN : angle 13.60546 / 7.16 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 267 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.7521 (mttt) cc_final: 0.7150 (tttt) REVERT: A 196 TRP cc_start: 0.7924 (m-10) cc_final: 0.6902 (m100) REVERT: A 250 LYS cc_start: 0.8226 (mmmm) cc_final: 0.7946 (mmmt) REVERT: A 705 MET cc_start: 0.6063 (mmp) cc_final: 0.5273 (mmp) REVERT: A 754 ASN cc_start: 0.7961 (t0) cc_final: 0.7496 (t0) REVERT: A 777 TYR cc_start: 0.6127 (m-80) cc_final: 0.5619 (m-80) REVERT: A 905 THR cc_start: 0.8066 (t) cc_final: 0.7281 (m) REVERT: A 1218 LEU cc_start: 0.8148 (mm) cc_final: 0.7948 (mp) REVERT: A 1219 LEU cc_start: 0.7781 (mt) cc_final: 0.7496 (tp) REVERT: A 1500 MET cc_start: 0.7024 (ttm) cc_final: 0.6743 (ttp) REVERT: A 1769 TYR cc_start: 0.6516 (OUTLIER) cc_final: 0.6041 (t80) REVERT: A 1777 PHE cc_start: 0.5581 (OUTLIER) cc_final: 0.5327 (t80) outliers start: 26 outliers final: 13 residues processed: 286 average time/residue: 0.0846 time to fit residues: 34.7108 Evaluate side-chains 224 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 1367 ASN Chi-restraints excluded: chain A residue 1376 ASN Chi-restraints excluded: chain A residue 1470 VAL Chi-restraints excluded: chain A residue 1473 ASP Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1769 TYR Chi-restraints excluded: chain A residue 1772 ILE Chi-restraints excluded: chain A residue 1774 LEU Chi-restraints excluded: chain A residue 1777 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN A 151 GLN A 303 ASN A 407 ASN A 420 GLN A 421 ASN A 865 ASN A1368 GLN A1445 ASN ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1493 GLN A1543 ASN A1701 ASN ** A1724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1733 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.206820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.169950 restraints weight = 11248.564| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.77 r_work: 0.3819 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 9804 Z= 0.175 Angle : 0.803 12.464 13309 Z= 0.383 Chirality : 0.044 0.344 1561 Planarity : 0.006 0.106 1561 Dihedral : 15.280 176.680 1460 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.48 % Favored : 93.16 % Rotamer: Outliers : 4.30 % Allowed : 15.09 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.09 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.24), residues: 1126 helix: -0.12 (0.18), residues: 806 sheet: None (None), residues: 0 loop : -2.63 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1305 TYR 0.018 0.002 TYR A 308 PHE 0.021 0.002 PHE A1618 TRP 0.027 0.001 TRP A 302 HIS 0.010 0.002 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 ( 9788) covalent geometry : angle 0.77204 / 0.37 (13276) SS BOND : bond 0.02371 / 1.13 ( 3) SS BOND : angle 5.03615 / 2.58 ( 6) hydrogen bonds : bond 0.04637 / 3.12 ( 625) hydrogen bonds : angle 5.02040 / 3.61 ( 1809) Misc. bond : bond 0.00709 / 0.37 ( 4) link_BETA1-4 : bond 0.02141 / 1.08 ( 4) link_BETA1-4 : angle 5.47422 / 3.07 ( 12) link_NAG-ASN : bond 0.00600 / 0.37 ( 5) link_NAG-ASN : angle 3.16483 / 1.79 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 242 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 TRP cc_start: 0.7993 (m-10) cc_final: 0.6905 (m100) REVERT: A 422 GLN cc_start: 0.8273 (tt0) cc_final: 0.7907 (tm-30) REVERT: A 777 TYR cc_start: 0.5977 (m-80) cc_final: 0.5176 (m-80) REVERT: A 905 THR cc_start: 0.8156 (t) cc_final: 0.7260 (m) REVERT: A 1215 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.6591 (t80) REVERT: A 1219 LEU cc_start: 0.7627 (mt) cc_final: 0.7342 (tp) REVERT: A 1427 MET cc_start: 0.8466 (mtp) cc_final: 0.8234 (mtm) REVERT: A 1445 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8460 (t0) REVERT: A 1500 MET cc_start: 0.6584 (ttm) cc_final: 0.6085 (ttp) REVERT: A 1729 TYR cc_start: 0.7038 (OUTLIER) cc_final: 0.6691 (m-80) REVERT: A 1763 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7894 (mp) REVERT: A 1777 PHE cc_start: 0.6326 (OUTLIER) cc_final: 0.5479 (t80) outliers start: 41 outliers final: 22 residues processed: 266 average time/residue: 0.0701 time to fit residues: 28.0692 Evaluate side-chains 230 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 785 PHE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 1215 PHE Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1376 ASN Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1388 SER Chi-restraints excluded: chain A residue 1445 ASN Chi-restraints excluded: chain A residue 1473 ASP Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1586 HIS Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1763 LEU Chi-restraints excluded: chain A residue 1777 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 74 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.203065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.165673 restraints weight = 11227.957| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 1.79 r_work: 0.3769 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 9804 Z= 0.226 Angle : 0.801 12.754 13309 Z= 0.386 Chirality : 0.044 0.196 1561 Planarity : 0.005 0.088 1561 Dihedral : 14.402 175.338 1446 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.10 % Favored : 92.81 % Rotamer: Outliers : 5.03 % Allowed : 17.92 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.09 % Twisted Proline : 3.23 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.24), residues: 1126 helix: 0.08 (0.18), residues: 807 sheet: None (None), residues: 0 loop : -2.59 (0.32), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1305 TYR 0.028 0.002 TYR A 379 PHE 0.024 0.002 PHE A 785 TRP 0.025 0.002 TRP A1442 HIS 0.008 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 ( 9788) covalent geometry : angle 0.78146 / 0.38 (13276) SS BOND : bond 0.00875 / 0.43 ( 3) SS BOND : angle 3.90118 / 1.96 ( 6) hydrogen bonds : bond 0.04595 / 3.04 ( 625) hydrogen bonds : angle 4.96287 / 3.57 ( 1809) Misc. bond : bond 0.00284 / 0.14 ( 4) link_BETA1-4 : bond 0.02014 / 1.02 ( 4) link_BETA1-4 : angle 4.56398 / 2.58 ( 12) link_NAG-ASN : bond 0.00439 / 0.28 ( 5) link_NAG-ASN : angle 2.52861 / 1.50 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 225 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 159 LYS cc_start: 0.7614 (mttt) cc_final: 0.7133 (ttmt) REVERT: A 196 TRP cc_start: 0.7956 (m-10) cc_final: 0.6997 (m100) REVERT: A 356 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8188 (m-80) REVERT: A 366 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7537 (mp) REVERT: A 422 GLN cc_start: 0.8291 (tt0) cc_final: 0.7934 (tm-30) REVERT: A 733 LEU cc_start: 0.8599 (mp) cc_final: 0.8357 (mp) REVERT: A 777 TYR cc_start: 0.6004 (m-80) cc_final: 0.5207 (m-80) REVERT: A 905 THR cc_start: 0.8168 (t) cc_final: 0.7300 (m) REVERT: A 1219 LEU cc_start: 0.7730 (mt) cc_final: 0.7410 (tp) REVERT: A 1227 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7581 (mt-10) REVERT: A 1729 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.6825 (m-80) REVERT: A 1777 PHE cc_start: 0.6224 (OUTLIER) cc_final: 0.5448 (t80) outliers start: 48 outliers final: 36 residues processed: 256 average time/residue: 0.0757 time to fit residues: 28.9333 Evaluate side-chains 243 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 725 THR Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 785 PHE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1366 ILE Chi-restraints excluded: chain A residue 1376 ASN Chi-restraints excluded: chain A residue 1379 ILE Chi-restraints excluded: chain A residue 1388 SER Chi-restraints excluded: chain A residue 1406 ASN Chi-restraints excluded: chain A residue 1473 ASP Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1564 LYS Chi-restraints excluded: chain A residue 1654 MET Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1763 LEU Chi-restraints excluded: chain A residue 1777 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 23 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 56 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 731 ASN ** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.207290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.170086 restraints weight = 11261.324| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 1.86 r_work: 0.3863 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3743 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 9804 Z= 0.154 Angle : 0.721 11.200 13309 Z= 0.346 Chirality : 0.041 0.203 1561 Planarity : 0.004 0.068 1561 Dihedral : 13.379 170.514 1446 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.48 % Favored : 93.34 % Rotamer: Outliers : 4.72 % Allowed : 19.08 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.09 % Twisted Proline : 3.23 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.25), residues: 1126 helix: 0.39 (0.18), residues: 812 sheet: None (None), residues: 0 loop : -2.52 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 812 TYR 0.016 0.002 TYR A 379 PHE 0.022 0.002 PHE A 785 TRP 0.027 0.002 TRP A1442 HIS 0.006 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 9788) covalent geometry : angle 0.70423 / 0.34 (13276) SS BOND : bond 0.00812 / 0.39 ( 3) SS BOND : angle 3.11913 / 1.46 ( 6) hydrogen bonds : bond 0.04168 / 2.80 ( 625) hydrogen bonds : angle 4.74058 / 3.40 ( 1809) Misc. bond : bond 0.00403 / 0.20 ( 4) link_BETA1-4 : bond 0.01595 / 0.81 ( 4) link_BETA1-4 : angle 4.18036 / 2.36 ( 12) link_NAG-ASN : bond 0.00453 / 0.28 ( 5) link_NAG-ASN : angle 2.22209 / 1.34 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 228 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 CYS cc_start: 0.5836 (OUTLIER) cc_final: 0.5496 (t) REVERT: A 196 TRP cc_start: 0.7914 (m-10) cc_final: 0.6998 (m100) REVERT: A 356 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.8090 (m-80) REVERT: A 422 GLN cc_start: 0.8230 (tt0) cc_final: 0.7854 (tm-30) REVERT: A 713 PHE cc_start: 0.6678 (m-80) cc_final: 0.6365 (t80) REVERT: A 733 LEU cc_start: 0.8626 (mp) cc_final: 0.8351 (mp) REVERT: A 745 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6987 (mm-30) REVERT: A 777 TYR cc_start: 0.5884 (m-80) cc_final: 0.5095 (m-80) REVERT: A 905 THR cc_start: 0.8208 (t) cc_final: 0.7329 (m) REVERT: A 1218 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7639 (mp) REVERT: A 1219 LEU cc_start: 0.7728 (mt) cc_final: 0.7438 (tp) REVERT: A 1227 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7235 (mt-10) REVERT: A 1637 ARG cc_start: 0.8371 (mmm-85) cc_final: 0.8130 (tpp80) REVERT: A 1729 TYR cc_start: 0.7142 (OUTLIER) cc_final: 0.6812 (m-80) REVERT: A 1763 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7828 (mp) REVERT: A 1767 ASN cc_start: 0.8032 (m-40) cc_final: 0.7338 (m-40) REVERT: A 1777 PHE cc_start: 0.6093 (OUTLIER) cc_final: 0.5244 (t80) outliers start: 45 outliers final: 30 residues processed: 259 average time/residue: 0.0678 time to fit residues: 26.3365 Evaluate side-chains 249 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 734 PHE Chi-restraints excluded: chain A residue 785 PHE Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1340 LEU Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1376 ASN Chi-restraints excluded: chain A residue 1388 SER Chi-restraints excluded: chain A residue 1406 ASN Chi-restraints excluded: chain A residue 1473 ASP Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1654 MET Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1763 LEU Chi-restraints excluded: chain A residue 1777 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 53 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 84 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 46 optimal weight: 0.0040 chunk 76 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 754 ASN ** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.211123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.174700 restraints weight = 11145.511| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 1.82 r_work: 0.3874 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9804 Z= 0.131 Angle : 0.683 10.248 13309 Z= 0.327 Chirality : 0.040 0.204 1561 Planarity : 0.004 0.058 1561 Dihedral : 12.289 169.672 1446 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.95 % Favored : 93.96 % Rotamer: Outliers : 4.93 % Allowed : 20.02 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.09 % Twisted Proline : 3.23 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.25), residues: 1126 helix: 0.62 (0.18), residues: 814 sheet: None (None), residues: 0 loop : -2.42 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 812 TYR 0.019 0.001 TYR A 169 PHE 0.020 0.001 PHE A 785 TRP 0.031 0.001 TRP A1442 HIS 0.005 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 9788) covalent geometry : angle 0.66746 / 0.32 (13276) SS BOND : bond 0.00451 / 0.22 ( 3) SS BOND : angle 2.68248 / 1.18 ( 6) hydrogen bonds : bond 0.03911 / 2.65 ( 625) hydrogen bonds : angle 4.54122 / 3.26 ( 1809) Misc. bond : bond 0.00226 / 0.11 ( 4) link_BETA1-4 : bond 0.01432 / 0.73 ( 4) link_BETA1-4 : angle 3.94751 / 2.23 ( 12) link_NAG-ASN : bond 0.00483 / 0.28 ( 5) link_NAG-ASN : angle 1.91151 / 1.16 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 231 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.7576 (mttt) cc_final: 0.7133 (ttmt) REVERT: A 196 TRP cc_start: 0.7908 (m-10) cc_final: 0.7004 (m100) REVERT: A 303 ASN cc_start: 0.4186 (OUTLIER) cc_final: 0.3220 (p0) REVERT: A 356 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: A 422 GLN cc_start: 0.8110 (tt0) cc_final: 0.7709 (tm-30) REVERT: A 733 LEU cc_start: 0.8721 (mp) cc_final: 0.8456 (mp) REVERT: A 734 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7855 (m-80) REVERT: A 777 TYR cc_start: 0.5983 (m-80) cc_final: 0.5110 (m-80) REVERT: A 905 THR cc_start: 0.8178 (t) cc_final: 0.7309 (m) REVERT: A 1218 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7675 (mp) REVERT: A 1219 LEU cc_start: 0.7774 (mt) cc_final: 0.7479 (tp) REVERT: A 1227 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7151 (mt-10) REVERT: A 1373 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6229 (mt) REVERT: A 1376 ASN cc_start: 0.2636 (OUTLIER) cc_final: 0.2280 (t0) REVERT: A 1581 MET cc_start: 0.7484 (mtt) cc_final: 0.7220 (mtt) REVERT: A 1729 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.6915 (m-80) REVERT: A 1763 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.8000 (mp) REVERT: A 1767 ASN cc_start: 0.7974 (m-40) cc_final: 0.7758 (m-40) REVERT: A 1777 PHE cc_start: 0.6130 (OUTLIER) cc_final: 0.5172 (t80) outliers start: 47 outliers final: 21 residues processed: 262 average time/residue: 0.0763 time to fit residues: 29.8823 Evaluate side-chains 246 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 734 PHE Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 785 PHE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1376 ASN Chi-restraints excluded: chain A residue 1388 SER Chi-restraints excluded: chain A residue 1406 ASN Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1654 MET Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1763 LEU Chi-restraints excluded: chain A residue 1777 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 10 optimal weight: 0.0670 chunk 41 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.209465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.172956 restraints weight = 11231.761| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.83 r_work: 0.3872 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9804 Z= 0.149 Angle : 0.691 10.026 13309 Z= 0.333 Chirality : 0.040 0.206 1561 Planarity : 0.004 0.054 1561 Dihedral : 11.627 144.075 1443 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.57 % Favored : 93.34 % Rotamer: Outliers : 4.61 % Allowed : 21.38 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.09 % Twisted Proline : 3.23 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.25), residues: 1126 helix: 0.68 (0.18), residues: 807 sheet: None (None), residues: 0 loop : -2.44 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 223 TYR 0.019 0.001 TYR A 379 PHE 0.026 0.002 PHE A1753 TRP 0.032 0.001 TRP A1442 HIS 0.004 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 9788) covalent geometry : angle 0.67551 / 0.33 (13276) SS BOND : bond 0.01088 / 0.52 ( 3) SS BOND : angle 2.71351 / 1.15 ( 6) hydrogen bonds : bond 0.03911 / 2.64 ( 625) hydrogen bonds : angle 4.54934 / 3.26 ( 1809) Misc. bond : bond 0.00467 / 0.23 ( 4) link_BETA1-4 : bond 0.01386 / 0.71 ( 4) link_BETA1-4 : angle 4.00206 / 2.25 ( 12) link_NAG-ASN : bond 0.00376 / 0.22 ( 5) link_NAG-ASN : angle 1.91294 / 1.16 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.7622 (mttt) cc_final: 0.7183 (ttmt) REVERT: A 196 TRP cc_start: 0.7875 (m-10) cc_final: 0.6945 (m100) REVERT: A 356 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8035 (m-80) REVERT: A 395 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7801 (ptt) REVERT: A 417 TYR cc_start: 0.7809 (t80) cc_final: 0.7482 (t80) REVERT: A 422 GLN cc_start: 0.8133 (tt0) cc_final: 0.7758 (tm-30) REVERT: A 733 LEU cc_start: 0.8699 (mp) cc_final: 0.8391 (mp) REVERT: A 777 TYR cc_start: 0.5813 (m-80) cc_final: 0.5006 (m-80) REVERT: A 905 THR cc_start: 0.8146 (t) cc_final: 0.7269 (m) REVERT: A 1218 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7518 (mp) REVERT: A 1219 LEU cc_start: 0.7698 (mt) cc_final: 0.7413 (tp) REVERT: A 1227 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7397 (mt-10) REVERT: A 1376 ASN cc_start: 0.2455 (OUTLIER) cc_final: 0.2039 (t0) REVERT: A 1729 TYR cc_start: 0.7201 (OUTLIER) cc_final: 0.6867 (m-80) REVERT: A 1763 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7864 (mp) REVERT: A 1767 ASN cc_start: 0.7984 (m-40) cc_final: 0.7754 (m-40) REVERT: A 1777 PHE cc_start: 0.6160 (OUTLIER) cc_final: 0.5170 (t80) outliers start: 44 outliers final: 30 residues processed: 248 average time/residue: 0.0777 time to fit residues: 28.3655 Evaluate side-chains 246 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 785 PHE Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1376 ASN Chi-restraints excluded: chain A residue 1388 SER Chi-restraints excluded: chain A residue 1406 ASN Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1564 LYS Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1654 MET Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1763 LEU Chi-restraints excluded: chain A residue 1777 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.210173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.173776 restraints weight = 11232.219| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 1.85 r_work: 0.3849 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9804 Z= 0.141 Angle : 0.677 10.257 13309 Z= 0.324 Chirality : 0.040 0.206 1561 Planarity : 0.004 0.053 1561 Dihedral : 11.081 121.516 1443 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.57 % Favored : 93.25 % Rotamer: Outliers : 4.51 % Allowed : 21.59 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.09 % Twisted Proline : 3.23 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.25), residues: 1126 helix: 0.74 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -2.36 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1637 TYR 0.017 0.001 TYR A 379 PHE 0.020 0.002 PHE A1753 TRP 0.035 0.001 TRP A1442 HIS 0.004 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9788) covalent geometry : angle 0.66364 / 0.32 (13276) SS BOND : bond 0.00373 / 0.19 ( 3) SS BOND : angle 2.71313 / 1.14 ( 6) hydrogen bonds : bond 0.03817 / 2.57 ( 625) hydrogen bonds : angle 4.46809 / 3.21 ( 1809) Misc. bond : bond 0.00204 / 0.10 ( 4) link_BETA1-4 : bond 0.01443 / 0.74 ( 4) link_BETA1-4 : angle 3.62349 / 2.00 ( 12) link_NAG-ASN : bond 0.00387 / 0.22 ( 5) link_NAG-ASN : angle 1.84381 / 1.12 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 220 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.7688 (mttt) cc_final: 0.7197 (ttmt) REVERT: A 196 TRP cc_start: 0.7909 (m-10) cc_final: 0.6984 (m100) REVERT: A 356 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7923 (m-80) REVERT: A 395 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7944 (ptt) REVERT: A 422 GLN cc_start: 0.8161 (tt0) cc_final: 0.7778 (tm-30) REVERT: A 905 THR cc_start: 0.8145 (t) cc_final: 0.7263 (m) REVERT: A 1219 LEU cc_start: 0.7773 (mt) cc_final: 0.7461 (tp) REVERT: A 1227 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7354 (mt-10) REVERT: A 1376 ASN cc_start: 0.2488 (OUTLIER) cc_final: 0.2011 (t0) REVERT: A 1729 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.6823 (m-80) REVERT: A 1767 ASN cc_start: 0.7918 (m-40) cc_final: 0.7516 (m-40) REVERT: A 1777 PHE cc_start: 0.6075 (OUTLIER) cc_final: 0.5088 (t80) outliers start: 43 outliers final: 30 residues processed: 250 average time/residue: 0.0739 time to fit residues: 27.1101 Evaluate side-chains 247 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 785 PHE Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 926 MET Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1376 ASN Chi-restraints excluded: chain A residue 1406 ASN Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1612 ASP Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1777 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 74 optimal weight: 20.0000 chunk 86 optimal weight: 0.0570 overall best weight: 4.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.204788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.166589 restraints weight = 11337.468| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 1.85 r_work: 0.3856 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 9804 Z= 0.261 Angle : 0.802 10.876 13309 Z= 0.386 Chirality : 0.045 0.266 1561 Planarity : 0.004 0.055 1561 Dihedral : 11.811 124.958 1443 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.37 % Favored : 92.45 % Rotamer: Outliers : 4.82 % Allowed : 22.12 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.09 % Twisted Proline : 3.23 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.25), residues: 1126 helix: 0.47 (0.18), residues: 807 sheet: -2.78 (1.69), residues: 12 loop : -2.37 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 384 TYR 0.037 0.002 TYR A 379 PHE 0.025 0.003 PHE A 394 TRP 0.033 0.002 TRP A1442 HIS 0.006 0.002 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.26 ( 9788) covalent geometry : angle 0.78698 / 0.38 (13276) SS BOND : bond 0.00887 / 0.44 ( 3) SS BOND : angle 3.43963 / 1.48 ( 6) hydrogen bonds : bond 0.04387 / 2.91 ( 625) hydrogen bonds : angle 4.78182 / 3.42 ( 1809) Misc. bond : bond 0.00242 / 0.12 ( 4) link_BETA1-4 : bond 0.01456 / 0.75 ( 4) link_BETA1-4 : angle 3.85636 / 2.12 ( 12) link_NAG-ASN : bond 0.00332 / 0.20 ( 5) link_NAG-ASN : angle 2.33009 / 1.39 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 199 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8194 (tt) cc_final: 0.7873 (tt) REVERT: A 159 LYS cc_start: 0.7709 (mttt) cc_final: 0.7255 (ttmt) REVERT: A 196 TRP cc_start: 0.7971 (m-10) cc_final: 0.6999 (m100) REVERT: A 417 TYR cc_start: 0.7919 (t80) cc_final: 0.7593 (t80) REVERT: A 422 GLN cc_start: 0.8176 (tt0) cc_final: 0.7841 (tm-30) REVERT: A 905 THR cc_start: 0.8382 (t) cc_final: 0.7441 (m) REVERT: A 1215 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.6525 (t80) REVERT: A 1219 LEU cc_start: 0.8096 (mt) cc_final: 0.7656 (tp) REVERT: A 1227 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7474 (mt-10) REVERT: A 1376 ASN cc_start: 0.2731 (OUTLIER) cc_final: 0.2415 (t0) REVERT: A 1597 ASP cc_start: 0.7930 (m-30) cc_final: 0.7656 (m-30) REVERT: A 1729 TYR cc_start: 0.7208 (OUTLIER) cc_final: 0.6878 (m-80) REVERT: A 1777 PHE cc_start: 0.6075 (OUTLIER) cc_final: 0.5100 (t80) outliers start: 46 outliers final: 36 residues processed: 225 average time/residue: 0.0714 time to fit residues: 24.1177 Evaluate side-chains 235 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 785 PHE Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 926 MET Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1215 PHE Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1376 ASN Chi-restraints excluded: chain A residue 1406 ASN Chi-restraints excluded: chain A residue 1466 LEU Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1654 MET Chi-restraints excluded: chain A residue 1711 THR Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1777 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 16 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 0.0270 chunk 101 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 overall best weight: 1.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 ASN A 420 GLN ** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.206372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.169613 restraints weight = 11198.844| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 1.84 r_work: 0.3858 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9804 Z= 0.156 Angle : 0.705 10.425 13309 Z= 0.336 Chirality : 0.041 0.206 1561 Planarity : 0.004 0.053 1561 Dihedral : 11.210 115.888 1443 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.39 % Favored : 93.52 % Rotamer: Outliers : 3.88 % Allowed : 23.48 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.09 % Twisted Proline : 3.23 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.25), residues: 1126 helix: 0.64 (0.18), residues: 806 sheet: -2.63 (1.63), residues: 12 loop : -2.24 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 341 TYR 0.019 0.002 TYR A 379 PHE 0.023 0.002 PHE A1522 TRP 0.026 0.001 TRP A1442 HIS 0.005 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 9788) covalent geometry : angle 0.69160 / 0.33 (13276) SS BOND : bond 0.00986 / 0.47 ( 3) SS BOND : angle 2.10631 / 1.24 ( 6) hydrogen bonds : bond 0.03972 / 2.66 ( 625) hydrogen bonds : angle 4.55935 / 3.27 ( 1809) Misc. bond : bond 0.00173 / 0.09 ( 4) link_BETA1-4 : bond 0.01478 / 0.76 ( 4) link_BETA1-4 : angle 3.69069 / 2.03 ( 12) link_NAG-ASN : bond 0.00336 / 0.20 ( 5) link_NAG-ASN : angle 2.09367 / 1.27 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8121 (tt) cc_final: 0.7804 (tt) REVERT: A 159 LYS cc_start: 0.7707 (mttt) cc_final: 0.7218 (ttmt) REVERT: A 196 TRP cc_start: 0.7925 (m-10) cc_final: 0.6948 (m100) REVERT: A 395 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7849 (ptt) REVERT: A 417 TYR cc_start: 0.7844 (t80) cc_final: 0.7565 (t80) REVERT: A 422 GLN cc_start: 0.8142 (tt0) cc_final: 0.7755 (tm-30) REVERT: A 1219 LEU cc_start: 0.7976 (mt) cc_final: 0.7527 (tp) REVERT: A 1227 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7384 (mt-10) REVERT: A 1376 ASN cc_start: 0.2574 (OUTLIER) cc_final: 0.2206 (t0) REVERT: A 1597 ASP cc_start: 0.7844 (m-30) cc_final: 0.7582 (m-30) REVERT: A 1729 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.6977 (m-80) REVERT: A 1762 PHE cc_start: 0.8771 (t80) cc_final: 0.8459 (t80) REVERT: A 1767 ASN cc_start: 0.7993 (m-40) cc_final: 0.7609 (m-40) REVERT: A 1777 PHE cc_start: 0.6060 (OUTLIER) cc_final: 0.5032 (t80) outliers start: 37 outliers final: 31 residues processed: 232 average time/residue: 0.0707 time to fit residues: 24.9405 Evaluate side-chains 233 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 785 PHE Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 926 MET Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1376 ASN Chi-restraints excluded: chain A residue 1406 ASN Chi-restraints excluded: chain A residue 1466 LEU Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1602 ILE Chi-restraints excluded: chain A residue 1612 ASP Chi-restraints excluded: chain A residue 1654 MET Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1777 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1439 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 = 0.4331 r_free = 0.4331 target = 0.204954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.168158 restraints weight = 11181.105| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.85 r_work: 0.3842 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 9804 Z= 0.189 Angle : 0.746 10.338 13309 Z= 0.357 Chirality : 0.042 0.209 1561 Planarity : 0.004 0.054 1561 Dihedral : 11.210 110.238 1443 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.28 % Favored : 92.54 % Rotamer: Outliers : 3.98 % Allowed : 24.11 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.09 % Twisted Proline : 3.23 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.25), residues: 1126 helix: 0.55 (0.18), residues: 812 sheet: -2.58 (1.64), residues: 12 loop : -2.36 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 384 TYR 0.027 0.002 TYR A 379 PHE 0.025 0.002 PHE A1522 TRP 0.025 0.002 TRP A1442 HIS 0.005 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 ( 9788) covalent geometry : angle 0.73219 / 0.35 (13276) SS BOND : bond 0.00607 / 0.30 ( 3) SS BOND : angle 3.05774 / 1.29 ( 6) hydrogen bonds : bond 0.04104 / 2.73 ( 625) hydrogen bonds : angle 4.64154 / 3.32 ( 1809) Misc. bond : bond 0.00189 / 0.09 ( 4) link_BETA1-4 : bond 0.01453 / 0.74 ( 4) link_BETA1-4 : angle 3.72538 / 2.04 ( 12) link_NAG-ASN : bond 0.00305 / 0.19 ( 5) link_NAG-ASN : angle 2.12513 / 1.28 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8151 (tt) cc_final: 0.7835 (tt) REVERT: A 159 LYS cc_start: 0.7684 (mttt) cc_final: 0.7203 (ttmt) REVERT: A 196 TRP cc_start: 0.7945 (m-10) cc_final: 0.6961 (m100) REVERT: A 395 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7857 (ptt) REVERT: A 417 TYR cc_start: 0.7811 (t80) cc_final: 0.7533 (t80) REVERT: A 422 GLN cc_start: 0.8139 (tt0) cc_final: 0.7791 (tm-30) REVERT: A 905 THR cc_start: 0.8262 (t) cc_final: 0.7381 (m) REVERT: A 1219 LEU cc_start: 0.7978 (mt) cc_final: 0.7539 (tp) REVERT: A 1227 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7419 (mt-10) REVERT: A 1376 ASN cc_start: 0.2888 (OUTLIER) cc_final: 0.2474 (t0) REVERT: A 1729 TYR cc_start: 0.7228 (OUTLIER) cc_final: 0.6986 (m-80) REVERT: A 1762 PHE cc_start: 0.8763 (t80) cc_final: 0.8444 (t80) REVERT: A 1767 ASN cc_start: 0.8062 (m-40) cc_final: 0.7635 (m-40) REVERT: A 1777 PHE cc_start: 0.6092 (OUTLIER) cc_final: 0.5080 (t80) outliers start: 38 outliers final: 32 residues processed: 225 average time/residue: 0.0659 time to fit residues: 22.3584 Evaluate side-chains 239 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 742 MET Chi-restraints excluded: chain A residue 785 PHE Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 926 MET Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1317 SER Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1376 ASN Chi-restraints excluded: chain A residue 1406 ASN Chi-restraints excluded: chain A residue 1466 LEU Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1516 LEU Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1612 ASP Chi-restraints excluded: chain A residue 1654 MET Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1777 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 47 optimal weight: 0.0170 chunk 76 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 overall best weight: 1.1220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1368 GLN A1406 ASN ** A1439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.208823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.172242 restraints weight = 11122.101| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 1.85 r_work: 0.3885 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3765 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9804 Z= 0.134 Angle : 0.699 10.509 13309 Z= 0.332 Chirality : 0.040 0.203 1561 Planarity : 0.004 0.052 1561 Dihedral : 10.773 104.010 1443 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.31 % Favored : 93.61 % Rotamer: Outliers : 3.56 % Allowed : 24.63 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.09 % Twisted Proline : 3.23 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.25), residues: 1126 helix: 0.68 (0.18), residues: 813 sheet: -2.50 (1.64), residues: 12 loop : -2.26 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 341 TYR 0.015 0.001 TYR A 379 PHE 0.028 0.002 PHE A1522 TRP 0.022 0.001 TRP A1442 HIS 0.004 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 9788) covalent geometry : angle 0.68688 / 0.33 (13276) SS BOND : bond 0.00641 / 0.31 ( 3) SS BOND : angle 1.95550 / 1.14 ( 6) hydrogen bonds : bond 0.03898 / 2.62 ( 625) hydrogen bonds : angle 4.49629 / 3.23 ( 1809) Misc. bond : bond 0.00129 / 0.06 ( 4) link_BETA1-4 : bond 0.01421 / 0.73 ( 4) link_BETA1-4 : angle 3.56599 / 1.95 ( 12) link_NAG-ASN : bond 0.00390 / 0.22 ( 5) link_NAG-ASN : angle 1.93211 / 1.18 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2601.29 seconds wall clock time: 45 minutes 4.79 seconds (2704.79 seconds total)