Starting phenix.real_space_refine on Wed Mar 4 12:40:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oz1_71047/03_2026/9oz1_71047_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oz1_71047/03_2026/9oz1_71047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oz1_71047/03_2026/9oz1_71047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oz1_71047/03_2026/9oz1_71047.map" model { file = "/net/cci-nas-00/data/ceres_data/9oz1_71047/03_2026/9oz1_71047_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oz1_71047/03_2026/9oz1_71047_trim.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 21 5.16 5 C 4163 2.51 5 N 1051 2.21 5 O 1287 1.98 5 H 6182 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12704 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 12441 Classifications: {'peptide': 780} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 736} Chain breaks: 5 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 2.24, per 1000 atoms: 0.18 Number of scatterers: 12704 At special positions: 0 Unit cell: (112.1, 101.48, 204.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 O 1287 8.00 N 1051 7.00 C 4163 6.00 H 6182 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A1336 " - pdb=" SG CYS A1378 " distance=2.03 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1380 " distance=2.03 Simple disulfide: pdb=" SG CYS A1453 " - pdb=" SG CYS A1486 " distance=2.03 Simple disulfide: pdb=" SG CYS A1721 " - pdb=" SG CYS A1729 " distance=2.04 Simple disulfide: pdb=" SG CYS A1825 " - pdb=" SG CYS A1829 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2401 " - " ASN A1233 " " NAG A2402 " - " ASN A1255 " " NAG A2403 " - " ASN A1282 " " NAG A2404 " - " ASN A1696 " " NAG A2405 " - " ASN A1730 " " NAG A2406 " - " ASN A1795 " " NAG A2407 " - " ASN A1822 " " NAG A2408 " - " ASN A1588 " " NAG A2409 " - " ASN A1628 " " NAG A2410 " - " ASN A1316 " " NAG B 1 " - " ASN A1110 " " NAG C 1 " - " ASN A1180 " " NAG D 1 " - " ASN A1470 " " NAG E 1 " - " ASN A1682 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 313.3 milliseconds 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 21 sheets defined 4.7% alpha, 44.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 1228 through 1232 Processing helix chain 'A' and resid 1314 through 1317 Processing helix chain 'A' and resid 1327 through 1334 removed outlier: 3.608A pdb=" N GLU A1330 " --> pdb=" O SER A1327 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A1333 " --> pdb=" O GLU A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1343 No H-bonds generated for 'chain 'A' and resid 1341 through 1343' Processing helix chain 'A' and resid 1442 through 1446 Processing helix chain 'A' and resid 1450 through 1454 Processing helix chain 'A' and resid 1600 through 1603 Processing helix chain 'A' and resid 1624 through 1626 No H-bonds generated for 'chain 'A' and resid 1624 through 1626' Processing sheet with id=AA1, first strand: chain 'A' and resid 1056 through 1060 Processing sheet with id=AA2, first strand: chain 'A' and resid 1112 through 1114 removed outlier: 4.314A pdb=" N GLN A1089 " --> pdb=" O PHE A1139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1181 through 1187 removed outlier: 6.895A pdb=" N LEU A1174 " --> pdb=" O ILE A1183 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU A1185 " --> pdb=" O LEU A1172 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU A1172 " --> pdb=" O GLU A1185 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A1166 " --> pdb=" O PHE A1173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1192 through 1198 removed outlier: 7.022A pdb=" N ILE A1207 " --> pdb=" O LYS A1193 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE A1195 " --> pdb=" O TYR A1205 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR A1205 " --> pdb=" O ILE A1195 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR A1197 " --> pdb=" O LYS A1203 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS A1203 " --> pdb=" O TYR A1197 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR A1206 " --> pdb=" O PHE A1213 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU A1212 " --> pdb=" O LEU A1225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1234 through 1240 removed outlier: 6.695A pdb=" N ALA A1249 " --> pdb=" O THR A1235 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE A1237 " --> pdb=" O PHE A1247 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE A1247 " --> pdb=" O ILE A1237 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL A1239 " --> pdb=" O HIS A1245 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N HIS A1245 " --> pdb=" O VAL A1239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1284 through 1285 removed outlier: 3.556A pdb=" N THR A1284 " --> pdb=" O GLU A1302 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU A1302 " --> pdb=" O THR A1284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1284 through 1285 removed outlier: 3.556A pdb=" N THR A1284 " --> pdb=" O GLU A1302 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU A1302 " --> pdb=" O THR A1284 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1345 through 1352 removed outlier: 5.291A pdb=" N ILE A1364 " --> pdb=" O GLY A1346 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LEU A1362 " --> pdb=" O PRO A1348 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER A1350 " --> pdb=" O GLN A1360 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLN A1360 " --> pdb=" O SER A1350 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A1384 " --> pdb=" O ILE A1370 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1393 through 1394 removed outlier: 3.513A pdb=" N THR A1398 " --> pdb=" O TYR A1405 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1393 through 1394 removed outlier: 6.515A pdb=" N THR A1414 " --> pdb=" O LYS A1431 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS A1431 " --> pdb=" O THR A1414 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A1416 " --> pdb=" O GLN A1429 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1456 through 1458 Processing sheet with id=AB3, first strand: chain 'A' and resid 1464 through 1468 removed outlier: 3.959A pdb=" N THR A1464 " --> pdb=" O SER A1476 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR A1474 " --> pdb=" O LEU A1466 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR A1468 " --> pdb=" O SER A1472 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER A1472 " --> pdb=" O THR A1468 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1520 through 1524 Processing sheet with id=AB5, first strand: chain 'A' and resid 1577 through 1583 removed outlier: 6.581A pdb=" N THR A1586 " --> pdb=" O LEU A1582 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1615 through 1622 removed outlier: 9.296A pdb=" N VAL A1610 " --> pdb=" O PRO A1617 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ALA A1619 " --> pdb=" O ILE A1608 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE A1608 " --> pdb=" O ALA A1619 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A1605 " --> pdb=" O PHE A1651 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1615 through 1622 removed outlier: 9.296A pdb=" N VAL A1610 " --> pdb=" O PRO A1617 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ALA A1619 " --> pdb=" O ILE A1608 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N ILE A1608 " --> pdb=" O ALA A1619 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A1605 " --> pdb=" O PHE A1651 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1676 through 1680 removed outlier: 4.369A pdb=" N ILE A1678 " --> pdb=" O GLN A1686 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN A1686 " --> pdb=" O ILE A1678 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N SER A1684 " --> pdb=" O PRO A1680 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A1730 " --> pdb=" O THR A1720 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A1718 " --> pdb=" O THR A1732 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1695 through 1706 removed outlier: 6.451A pdb=" N VAL A1747 " --> pdb=" O ASN A1696 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N THR A1698 " --> pdb=" O THR A1745 " (cutoff:3.500A) removed outlier: 10.014A pdb=" N THR A1745 " --> pdb=" O THR A1698 " (cutoff:3.500A) removed outlier: 9.808A pdb=" N PHE A1700 " --> pdb=" O ARG A1743 " (cutoff:3.500A) removed outlier: 11.126A pdb=" N ARG A1743 " --> pdb=" O PHE A1700 " (cutoff:3.500A) removed outlier: 9.420A pdb=" N PHE A1702 " --> pdb=" O LEU A1741 " (cutoff:3.500A) removed outlier: 10.794A pdb=" N LEU A1741 " --> pdb=" O PHE A1702 " (cutoff:3.500A) removed outlier: 9.798A pdb=" N LEU A1704 " --> pdb=" O ASN A1739 " (cutoff:3.500A) removed outlier: 11.064A pdb=" N ASN A1739 " --> pdb=" O LEU A1704 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1695 through 1706 removed outlier: 6.451A pdb=" N VAL A1747 " --> pdb=" O ASN A1696 " (cutoff:3.500A) removed outlier: 9.792A pdb=" N THR A1698 " --> pdb=" O THR A1745 " (cutoff:3.500A) removed outlier: 10.014A pdb=" N THR A1745 " --> pdb=" O THR A1698 " (cutoff:3.500A) removed outlier: 9.808A pdb=" N PHE A1700 " --> pdb=" O ARG A1743 " (cutoff:3.500A) removed outlier: 11.126A pdb=" N ARG A1743 " --> pdb=" O PHE A1700 " (cutoff:3.500A) removed outlier: 9.420A pdb=" N PHE A1702 " --> pdb=" O LEU A1741 " (cutoff:3.500A) removed outlier: 10.794A pdb=" N LEU A1741 " --> pdb=" O PHE A1702 " (cutoff:3.500A) removed outlier: 9.798A pdb=" N LEU A1704 " --> pdb=" O ASN A1739 " (cutoff:3.500A) removed outlier: 11.064A pdb=" N ASN A1739 " --> pdb=" O LEU A1704 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1775 through 1777 removed outlier: 4.029A pdb=" N SER A1783 " --> pdb=" O ALA A1777 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS A1829 " --> pdb=" O TRP A1786 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1818 through 1823 removed outlier: 5.189A pdb=" N VAL A1819 " --> pdb=" O SER A1803 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER A1803 " --> pdb=" O VAL A1819 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR A1821 " --> pdb=" O LEU A1801 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A1801 " --> pdb=" O TYR A1821 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR A1798 " --> pdb=" O ALA A1847 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA A1844 " --> pdb=" O TYR A1855 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR A1855 " --> pdb=" O ALA A1844 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ALA A1846 " --> pdb=" O GLY A1853 " (cutoff:3.500A) 189 hydrogen bonds defined for protein. 462 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: 3.19 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6180 1.03 - 1.23: 162 1.23 - 1.43: 2667 1.43 - 1.62: 3817 1.62 - 1.82: 30 Bond restraints: 12856 Sorted by residual: bond pdb=" C SER A1488 " pdb=" N ILE A1489 " ideal model delta sigma weight residual 1.332 1.308 0.024 1.73e-02 3.34e+03 1.85e+00 bond pdb=" CA CYS A1486 " pdb=" CB CYS A1486 " ideal model delta sigma weight residual 1.525 1.535 -0.010 8.30e-03 1.45e+04 1.42e+00 bond pdb=" CA LEU A1096 " pdb=" CB LEU A1096 " ideal model delta sigma weight residual 1.527 1.499 0.028 2.48e-02 1.63e+03 1.31e+00 bond pdb=" C ASN A1084 " pdb=" N GLY A1085 " ideal model delta sigma weight residual 1.327 1.319 0.008 8.10e-03 1.52e+04 9.63e-01 bond pdb=" CA CYS A1721 " pdb=" HA CYS A1721 " ideal model delta sigma weight residual 0.970 0.951 0.019 2.00e-02 2.50e+03 9.31e-01 ... (remaining 12851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 21630 1.01 - 2.03: 1377 2.03 - 3.04: 70 3.04 - 4.05: 39 4.05 - 5.06: 2 Bond angle restraints: 23118 Sorted by residual: angle pdb=" N LEU A1454 " pdb=" CA LEU A1454 " pdb=" C LEU A1454 " ideal model delta sigma weight residual 114.56 111.17 3.39 1.27e+00 6.20e-01 7.12e+00 angle pdb=" N CYS A1729 " pdb=" CA CYS A1729 " pdb=" C CYS A1729 " ideal model delta sigma weight residual 108.60 112.24 -3.64 1.46e+00 4.69e-01 6.21e+00 angle pdb=" C THR A1728 " pdb=" N CYS A1729 " pdb=" CA CYS A1729 " ideal model delta sigma weight residual 121.80 117.94 3.86 1.71e+00 3.42e-01 5.11e+00 angle pdb=" N ASN A1433 " pdb=" CA ASN A1433 " pdb=" C ASN A1433 " ideal model delta sigma weight residual 112.97 110.65 2.32 1.06e+00 8.90e-01 4.77e+00 angle pdb=" N VAL A1820 " pdb=" CA VAL A1820 " pdb=" C VAL A1820 " ideal model delta sigma weight residual 109.34 113.58 -4.24 2.08e+00 2.31e-01 4.16e+00 ... (remaining 23113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.03: 5894 14.03 - 28.05: 345 28.05 - 42.08: 96 42.08 - 56.11: 38 56.11 - 70.13: 8 Dihedral angle restraints: 6381 sinusoidal: 3624 harmonic: 2757 Sorted by residual: dihedral pdb=" CA ASN A1255 " pdb=" C ASN A1255 " pdb=" N GLU A1256 " pdb=" CA GLU A1256 " ideal model delta harmonic sigma weight residual -180.00 -155.97 -24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA TYR A1325 " pdb=" C TYR A1325 " pdb=" N GLU A1326 " pdb=" CA GLU A1326 " ideal model delta harmonic sigma weight residual 180.00 160.55 19.45 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA PHE A1173 " pdb=" C PHE A1173 " pdb=" N LEU A1174 " pdb=" CA LEU A1174 " ideal model delta harmonic sigma weight residual 180.00 162.31 17.69 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 6378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 947 0.055 - 0.109: 110 0.109 - 0.164: 35 0.164 - 0.219: 3 0.219 - 0.273: 1 Chirality restraints: 1096 Sorted by residual: chirality pdb=" C1 NAG A2404 " pdb=" ND2 ASN A1696 " pdb=" C2 NAG A2404 " pdb=" O5 NAG A2404 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C1 NAG A2403 " pdb=" ND2 ASN A1282 " pdb=" C2 NAG A2403 " pdb=" O5 NAG A2403 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" C1 NAG A2401 " pdb=" ND2 ASN A1233 " pdb=" C2 NAG A2401 " pdb=" O5 NAG A2401 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.35e-01 ... (remaining 1093 not shown) Planarity restraints: 1864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A1127 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO A1128 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A1128 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1128 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1773 " 0.019 5.00e-02 4.00e+02 2.89e-02 1.34e+00 pdb=" N PRO A1774 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A1774 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A1774 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A1535 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO A1536 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A1536 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A1536 " 0.016 5.00e-02 4.00e+02 ... (remaining 1861 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.45: 7570 2.45 - 2.99: 28369 2.99 - 3.52: 30449 3.52 - 4.06: 43627 4.06 - 4.60: 62287 Nonbonded interactions: 172302 Sorted by model distance: nonbonded pdb=" H LEU A1454 " pdb=" H THR A1455 " model vdw 1.912 2.100 nonbonded pdb=" H SER A1538 " pdb=" HG1 THR A1566 " model vdw 1.918 2.100 nonbonded pdb=" H THR A1566 " pdb=" HG1 THR A1566 " model vdw 1.930 2.100 nonbonded pdb=" HA CYS A1721 " pdb=" HB3 CYS A1729 " model vdw 1.948 2.440 nonbonded pdb=" HD3 ARG A1347 " pdb="HH11 ARG A1347 " model vdw 1.951 2.270 ... (remaining 172297 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' } 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 group one per residue 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: 2.850 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: 0.040 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 12.940 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 : 0.004 0.028 6698 Z= 0.180 Angle : 0.602 6.355 9159 Z= 0.334 Chirality : 0.043 0.273 1096 Planarity : 0.004 0.034 1119 Dihedral : 9.504 70.134 2733 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.28 % Allowed : 2.38 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.30), residues: 768 helix: -5.15 (0.30), residues: 13 sheet: -1.34 (0.31), residues: 287 loop : -0.85 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1382 TYR 0.016 0.001 TYR A1311 PHE 0.009 0.001 PHE A1261 TRP 0.008 0.001 TRP A1109 HIS 0.003 0.001 HIS A1652 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 6674) covalent geometry : angle 0.57511 ( 9092) SS BOND : bond 0.00310 ( 5) SS BOND : angle 1.12447 ( 10) hydrogen bonds : bond 0.22787 ( 179) hydrogen bonds : angle 12.11175 ( 462) link_BETA1-4 : bond 0.00645 ( 5) link_BETA1-4 : angle 2.04708 ( 15) link_NAG-ASN : bond 0.00399 ( 14) link_NAG-ASN : angle 2.37157 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1173 PHE cc_start: 0.7945 (m-80) cc_final: 0.7731 (m-10) REVERT: A 1276 ILE cc_start: 0.8727 (tp) cc_final: 0.8401 (tp) REVERT: A 1319 MET cc_start: 0.8596 (ttp) cc_final: 0.8076 (ttp) REVERT: A 1524 ILE cc_start: 0.9290 (tp) cc_final: 0.8984 (tt) outliers start: 2 outliers final: 0 residues processed: 56 average time/residue: 0.3026 time to fit residues: 20.6722 Evaluate side-chains 34 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1848 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.095591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.070446 restraints weight = 44125.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.074165 restraints weight = 19759.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.076613 restraints weight = 12204.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.078258 restraints weight = 8753.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.079230 restraints weight = 6916.532| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6698 Z= 0.182 Angle : 0.580 5.931 9159 Z= 0.298 Chirality : 0.045 0.232 1096 Planarity : 0.004 0.030 1119 Dihedral : 5.941 49.519 1236 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.42 % Allowed : 4.90 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.30), residues: 768 helix: -5.30 (0.26), residues: 13 sheet: -1.17 (0.30), residues: 293 loop : -0.98 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1560 TYR 0.017 0.001 TYR A1311 PHE 0.013 0.001 PHE A1261 TRP 0.007 0.001 TRP A1406 HIS 0.003 0.001 HIS A1652 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 6674) covalent geometry : angle 0.55586 ( 9092) SS BOND : bond 0.00478 ( 5) SS BOND : angle 2.29730 ( 10) hydrogen bonds : bond 0.04506 ( 179) hydrogen bonds : angle 8.48215 ( 462) link_BETA1-4 : bond 0.00424 ( 5) link_BETA1-4 : angle 1.42357 ( 15) link_NAG-ASN : bond 0.00328 ( 14) link_NAG-ASN : angle 2.10286 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1173 PHE cc_start: 0.7952 (m-80) cc_final: 0.7693 (m-10) REVERT: A 1319 MET cc_start: 0.8673 (ttp) cc_final: 0.8280 (ttp) REVERT: A 1524 ILE cc_start: 0.9262 (tp) cc_final: 0.8940 (tt) outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 0.2547 time to fit residues: 12.0487 Evaluate side-chains 32 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 42 optimal weight: 0.0770 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.095814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.070578 restraints weight = 44567.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.074399 restraints weight = 19875.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.076816 restraints weight = 12145.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.078326 restraints weight = 8777.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.079463 restraints weight = 7037.152| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6698 Z= 0.166 Angle : 0.551 5.923 9159 Z= 0.282 Chirality : 0.045 0.233 1096 Planarity : 0.004 0.029 1119 Dihedral : 5.948 50.892 1236 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.42 % Allowed : 5.03 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.30), residues: 768 helix: -5.28 (0.27), residues: 13 sheet: -1.04 (0.29), residues: 308 loop : -0.96 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1560 TYR 0.017 0.001 TYR A1311 PHE 0.013 0.001 PHE A1261 TRP 0.006 0.001 TRP A1406 HIS 0.003 0.001 HIS A1426 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 6674) covalent geometry : angle 0.52894 ( 9092) SS BOND : bond 0.00497 ( 5) SS BOND : angle 1.78758 ( 10) hydrogen bonds : bond 0.03699 ( 179) hydrogen bonds : angle 7.61451 ( 462) link_BETA1-4 : bond 0.00362 ( 5) link_BETA1-4 : angle 1.22525 ( 15) link_NAG-ASN : bond 0.00332 ( 14) link_NAG-ASN : angle 2.06600 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1173 PHE cc_start: 0.7923 (m-80) cc_final: 0.7663 (m-10) REVERT: A 1524 ILE cc_start: 0.9256 (tp) cc_final: 0.8935 (tt) REVERT: A 1786 TRP cc_start: 0.4923 (p90) cc_final: 0.4698 (p90) outliers start: 3 outliers final: 3 residues processed: 31 average time/residue: 0.2531 time to fit residues: 10.1036 Evaluate side-chains 32 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 0.3980 chunk 77 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.099980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.075300 restraints weight = 43164.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.079294 restraints weight = 19277.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.081814 restraints weight = 11784.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.083448 restraints weight = 8474.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.084351 restraints weight = 6683.881| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6698 Z= 0.165 Angle : 0.540 5.829 9159 Z= 0.277 Chirality : 0.044 0.227 1096 Planarity : 0.004 0.031 1119 Dihedral : 5.960 51.385 1236 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.84 % Allowed : 5.31 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.30), residues: 768 helix: -5.21 (0.32), residues: 13 sheet: -1.09 (0.29), residues: 308 loop : -0.96 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1560 TYR 0.017 0.001 TYR A1311 PHE 0.013 0.001 PHE A1261 TRP 0.006 0.001 TRP A1406 HIS 0.003 0.001 HIS A1426 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 6674) covalent geometry : angle 0.52026 ( 9092) SS BOND : bond 0.00374 ( 5) SS BOND : angle 1.54624 ( 10) hydrogen bonds : bond 0.03204 ( 179) hydrogen bonds : angle 7.04395 ( 462) link_BETA1-4 : bond 0.00384 ( 5) link_BETA1-4 : angle 1.15678 ( 15) link_NAG-ASN : bond 0.00325 ( 14) link_NAG-ASN : angle 1.99829 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1173 PHE cc_start: 0.7920 (m-80) cc_final: 0.7704 (m-10) REVERT: A 1524 ILE cc_start: 0.9249 (tp) cc_final: 0.8928 (tt) REVERT: A 1786 TRP cc_start: 0.5023 (p90) cc_final: 0.4811 (p90) outliers start: 6 outliers final: 4 residues processed: 34 average time/residue: 0.2406 time to fit residues: 10.5957 Evaluate side-chains 33 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1137 GLN Chi-restraints excluded: chain A residue 1238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 10 optimal weight: 0.9980 chunk 67 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.099868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.075257 restraints weight = 43458.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.079228 restraints weight = 19316.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.081749 restraints weight = 11791.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.083345 restraints weight = 8427.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.084428 restraints weight = 6655.076| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6698 Z= 0.150 Angle : 0.524 5.803 9159 Z= 0.268 Chirality : 0.044 0.226 1096 Planarity : 0.004 0.033 1119 Dihedral : 5.896 51.351 1236 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.56 % Allowed : 5.59 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.30), residues: 768 helix: -5.17 (0.35), residues: 13 sheet: -1.05 (0.29), residues: 314 loop : -0.91 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1560 TYR 0.016 0.001 TYR A1311 PHE 0.013 0.001 PHE A1261 TRP 0.006 0.001 TRP A1109 HIS 0.003 0.001 HIS A1181 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6674) covalent geometry : angle 0.50491 ( 9092) SS BOND : bond 0.00359 ( 5) SS BOND : angle 1.40250 ( 10) hydrogen bonds : bond 0.03036 ( 179) hydrogen bonds : angle 6.68715 ( 462) link_BETA1-4 : bond 0.00307 ( 5) link_BETA1-4 : angle 1.08988 ( 15) link_NAG-ASN : bond 0.00324 ( 14) link_NAG-ASN : angle 1.95306 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1173 PHE cc_start: 0.7939 (m-80) cc_final: 0.7712 (m-10) REVERT: A 1473 PHE cc_start: 0.8836 (m-10) cc_final: 0.8554 (m-10) REVERT: A 1524 ILE cc_start: 0.9196 (tp) cc_final: 0.8874 (tt) outliers start: 4 outliers final: 3 residues processed: 35 average time/residue: 0.2150 time to fit residues: 9.8437 Evaluate side-chains 33 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 33 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 0.0980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.099900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.074812 restraints weight = 43320.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.078954 restraints weight = 18668.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.081531 restraints weight = 11195.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.083226 restraints weight = 7963.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.084183 restraints weight = 6259.870| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6698 Z= 0.161 Angle : 0.524 5.791 9159 Z= 0.268 Chirality : 0.044 0.226 1096 Planarity : 0.004 0.035 1119 Dihedral : 5.909 51.382 1236 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.98 % Allowed : 5.31 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.30), residues: 768 helix: -5.14 (0.37), residues: 13 sheet: -1.05 (0.30), residues: 305 loop : -0.97 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1560 TYR 0.017 0.001 TYR A1311 PHE 0.013 0.001 PHE A1261 TRP 0.006 0.001 TRP A1406 HIS 0.003 0.001 HIS A1652 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6674) covalent geometry : angle 0.50475 ( 9092) SS BOND : bond 0.00347 ( 5) SS BOND : angle 1.34528 ( 10) hydrogen bonds : bond 0.02933 ( 179) hydrogen bonds : angle 6.54981 ( 462) link_BETA1-4 : bond 0.00305 ( 5) link_BETA1-4 : angle 1.09672 ( 15) link_NAG-ASN : bond 0.00325 ( 14) link_NAG-ASN : angle 1.94268 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1173 PHE cc_start: 0.7959 (m-80) cc_final: 0.7722 (m-10) REVERT: A 1473 PHE cc_start: 0.8774 (m-10) cc_final: 0.8489 (m-10) REVERT: A 1524 ILE cc_start: 0.9185 (tp) cc_final: 0.8860 (tt) outliers start: 7 outliers final: 6 residues processed: 39 average time/residue: 0.2098 time to fit residues: 10.8407 Evaluate side-chains 37 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1137 GLN Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1414 THR Chi-restraints excluded: chain A residue 1453 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.098664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.073848 restraints weight = 43459.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.077785 restraints weight = 19545.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.080294 restraints weight = 12024.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.081890 restraints weight = 8641.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.082812 restraints weight = 6849.380| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6698 Z= 0.230 Angle : 0.562 5.786 9159 Z= 0.288 Chirality : 0.045 0.229 1096 Planarity : 0.004 0.032 1119 Dihedral : 6.165 52.568 1236 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.84 % Allowed : 5.73 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.30), residues: 768 helix: -5.14 (0.37), residues: 13 sheet: -1.20 (0.29), residues: 310 loop : -1.07 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1690 TYR 0.017 0.001 TYR A1311 PHE 0.016 0.001 PHE A1261 TRP 0.010 0.001 TRP A1786 HIS 0.004 0.002 HIS A1426 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 6674) covalent geometry : angle 0.54199 ( 9092) SS BOND : bond 0.00504 ( 5) SS BOND : angle 1.66556 ( 10) hydrogen bonds : bond 0.03079 ( 179) hydrogen bonds : angle 6.58630 ( 462) link_BETA1-4 : bond 0.00287 ( 5) link_BETA1-4 : angle 1.12132 ( 15) link_NAG-ASN : bond 0.00385 ( 14) link_NAG-ASN : angle 2.06951 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1173 PHE cc_start: 0.8000 (m-80) cc_final: 0.7761 (m-10) REVERT: A 1473 PHE cc_start: 0.8839 (m-10) cc_final: 0.8554 (m-10) REVERT: A 1524 ILE cc_start: 0.9183 (tp) cc_final: 0.8862 (tt) outliers start: 6 outliers final: 6 residues processed: 36 average time/residue: 0.1746 time to fit residues: 8.5853 Evaluate side-chains 35 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1137 GLN Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1414 THR Chi-restraints excluded: chain A residue 1453 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.099736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.074774 restraints weight = 42951.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.078894 restraints weight = 18495.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.081403 restraints weight = 11136.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.083098 restraints weight = 7977.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.084104 restraints weight = 6272.314| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6698 Z= 0.149 Angle : 0.525 5.855 9159 Z= 0.268 Chirality : 0.044 0.226 1096 Planarity : 0.004 0.044 1119 Dihedral : 6.042 52.570 1236 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.98 % Allowed : 5.87 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.30), residues: 768 helix: -5.19 (0.33), residues: 13 sheet: -1.15 (0.30), residues: 305 loop : -1.02 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1560 TYR 0.016 0.001 TYR A1311 PHE 0.013 0.001 PHE A1261 TRP 0.006 0.001 TRP A1786 HIS 0.003 0.001 HIS A1181 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 6674) covalent geometry : angle 0.50539 ( 9092) SS BOND : bond 0.00495 ( 5) SS BOND : angle 1.65051 ( 10) hydrogen bonds : bond 0.02863 ( 179) hydrogen bonds : angle 6.39701 ( 462) link_BETA1-4 : bond 0.00307 ( 5) link_BETA1-4 : angle 1.06457 ( 15) link_NAG-ASN : bond 0.00342 ( 14) link_NAG-ASN : angle 1.93243 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1173 PHE cc_start: 0.7966 (m-80) cc_final: 0.7718 (m-10) REVERT: A 1473 PHE cc_start: 0.8774 (m-10) cc_final: 0.8495 (m-10) REVERT: A 1524 ILE cc_start: 0.9176 (tp) cc_final: 0.8849 (tt) outliers start: 7 outliers final: 7 residues processed: 38 average time/residue: 0.1935 time to fit residues: 9.8694 Evaluate side-chains 37 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1137 GLN Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1414 THR Chi-restraints excluded: chain A residue 1453 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.099846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.074777 restraints weight = 43356.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.078961 restraints weight = 18695.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.081556 restraints weight = 11215.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.083239 restraints weight = 7970.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.084272 restraints weight = 6279.689| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6698 Z= 0.151 Angle : 0.519 5.823 9159 Z= 0.265 Chirality : 0.044 0.225 1096 Planarity : 0.003 0.028 1119 Dihedral : 5.929 52.199 1236 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.26 % Allowed : 5.73 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.30), residues: 768 helix: -5.19 (0.33), residues: 13 sheet: -1.17 (0.29), residues: 308 loop : -1.00 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1560 TYR 0.016 0.001 TYR A1311 PHE 0.012 0.001 PHE A1261 TRP 0.009 0.001 TRP A1786 HIS 0.003 0.001 HIS A1181 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6674) covalent geometry : angle 0.50034 ( 9092) SS BOND : bond 0.00432 ( 5) SS BOND : angle 1.48408 ( 10) hydrogen bonds : bond 0.02785 ( 179) hydrogen bonds : angle 6.28508 ( 462) link_BETA1-4 : bond 0.00301 ( 5) link_BETA1-4 : angle 1.06954 ( 15) link_NAG-ASN : bond 0.00336 ( 14) link_NAG-ASN : angle 1.91289 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1173 PHE cc_start: 0.7968 (m-80) cc_final: 0.7715 (m-10) REVERT: A 1473 PHE cc_start: 0.8754 (m-10) cc_final: 0.8491 (m-10) REVERT: A 1524 ILE cc_start: 0.9109 (tp) cc_final: 0.8801 (tt) outliers start: 9 outliers final: 8 residues processed: 40 average time/residue: 0.1992 time to fit residues: 10.5977 Evaluate side-chains 38 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1137 GLN Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1300 ILE Chi-restraints excluded: chain A residue 1414 THR Chi-restraints excluded: chain A residue 1453 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.0070 chunk 22 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 0.0870 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.100641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.075608 restraints weight = 43173.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.079803 restraints weight = 18587.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.082394 restraints weight = 11149.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.084044 restraints weight = 7940.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.085150 restraints weight = 6247.133| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6698 Z= 0.112 Angle : 0.506 6.329 9159 Z= 0.258 Chirality : 0.044 0.221 1096 Planarity : 0.004 0.048 1119 Dihedral : 5.800 52.365 1236 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.98 % Allowed : 6.01 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.30), residues: 768 helix: -5.25 (0.29), residues: 13 sheet: -1.09 (0.30), residues: 303 loop : -0.97 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1560 TYR 0.015 0.001 TYR A1311 PHE 0.010 0.001 PHE A1261 TRP 0.007 0.001 TRP A1786 HIS 0.003 0.001 HIS A1181 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 6674) covalent geometry : angle 0.48845 ( 9092) SS BOND : bond 0.00357 ( 5) SS BOND : angle 1.43395 ( 10) hydrogen bonds : bond 0.02693 ( 179) hydrogen bonds : angle 6.15561 ( 462) link_BETA1-4 : bond 0.00329 ( 5) link_BETA1-4 : angle 1.06123 ( 15) link_NAG-ASN : bond 0.00341 ( 14) link_NAG-ASN : angle 1.82795 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1173 PHE cc_start: 0.7941 (m-80) cc_final: 0.7717 (m-10) REVERT: A 1473 PHE cc_start: 0.8711 (m-10) cc_final: 0.8466 (m-10) REVERT: A 1524 ILE cc_start: 0.9099 (tp) cc_final: 0.8787 (tt) outliers start: 7 outliers final: 6 residues processed: 37 average time/residue: 0.1745 time to fit residues: 8.7596 Evaluate side-chains 36 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1137 GLN Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1453 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 0.1980 chunk 6 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 26 optimal weight: 0.0170 chunk 57 optimal weight: 1.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.100807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.076219 restraints weight = 43347.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.080302 restraints weight = 19160.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.082745 restraints weight = 11559.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.084411 restraints weight = 8349.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.085403 restraints weight = 6576.823| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6698 Z= 0.113 Angle : 0.500 5.798 9159 Z= 0.254 Chirality : 0.044 0.220 1096 Planarity : 0.003 0.028 1119 Dihedral : 5.637 51.365 1236 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.98 % Allowed : 6.43 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.30), residues: 768 helix: -5.26 (0.28), residues: 13 sheet: -1.01 (0.29), residues: 308 loop : -0.90 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1560 TYR 0.016 0.001 TYR A1311 PHE 0.009 0.001 PHE A1261 TRP 0.009 0.001 TRP A1786 HIS 0.003 0.001 HIS A1181 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6674) covalent geometry : angle 0.48203 ( 9092) SS BOND : bond 0.00398 ( 5) SS BOND : angle 1.47464 ( 10) hydrogen bonds : bond 0.02649 ( 179) hydrogen bonds : angle 6.03307 ( 462) link_BETA1-4 : bond 0.00340 ( 5) link_BETA1-4 : angle 1.06398 ( 15) link_NAG-ASN : bond 0.00329 ( 14) link_NAG-ASN : angle 1.81395 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2613.36 seconds wall clock time: 45 minutes 1.09 seconds (2701.09 seconds total)