Starting phenix.real_space_refine on Sun May 3 18:22:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g1a_29665/05_2026/8g1a_29665.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g1a_29665/05_2026/8g1a_29665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g1a_29665/05_2026/8g1a_29665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g1a_29665/05_2026/8g1a_29665.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g1a_29665/05_2026/8g1a_29665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g1a_29665/05_2026/8g1a_29665.map" } resolution = 2.8 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= -0.002 sd= 0.064 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 P 19 5.49 5 S 99 5.16 5 C 9094 2.51 5 N 2064 2.21 5 O 2449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13725 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10366 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1282, 10356 Classifications: {'peptide': 1282} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 1240} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 1282, 10356 Classifications: {'peptide': 1282} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 1240} Chain breaks: 5 bond proxies already assigned to first conformer: 10593 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" Number of atoms: 983 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112} Conformer: "B" Number of residues, atoms: 119, 974 Classifications: {'peptide': 119} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112} bond proxies already assigned to first conformer: 984 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 828 Unusual residues: {'9Z9': 1, 'LPE': 11, 'NAG': 3, 'P0T': 2, 'PCW': 4, 'Y01': 5} Classifications: {'peptide': 2, 'undetermined': 26} Link IDs: {None: 27} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'P5S:plan-2': 1, 'P5S:plan-1': 1, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 76 Unusual residues: {'LPE': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A 14 " occ=0.55 ... (18 atoms not shown) pdb=" NE2BHIS A 14 " occ=0.45 Time building chain proxies: 4.88, per 1000 atoms: 0.36 Number of scatterers: 13725 At special positions: 0 Unit cell: (131.452, 139.25, 137.022, 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 99 16.00 P 19 15.00 O 2449 8.00 N 2064 7.00 C 9094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS C 55 " distance=2.03 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.03 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.03 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.03 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.02 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2001 " - " ASN A 283 " " NAG A2002 " - " ASN A1366 " " NAG A2003 " - " ASN A1375 " " NAG B 301 " - " ASN B 93 " " NAG B 302 " - " ASN B 110 " " NAG B 303 " - " ASN B 114 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN B 135 " Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 1.0 seconds 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3000 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 8 sheets defined 63.5% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 16 through 34 Processing helix chain 'A' and resid 50 through 54 removed outlier: 3.765A pdb=" N LEU A 53 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 54 " --> pdb=" O SER A 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 50 through 54' Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.900A pdb=" N ASP A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.544A pdb=" N MET A 108 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 125 through 144 removed outlier: 3.792A pdb=" N SER A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 164 removed outlier: 3.769A pdb=" N VAL A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 189 through 203 Processing helix chain 'A' and resid 209 through 216 removed outlier: 3.845A pdb=" N PHE A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 221 through 228 removed outlier: 4.081A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 245 Processing helix chain 'A' and resid 246 through 267 Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.613A pdb=" N LYS A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 362 through 374 removed outlier: 3.863A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.720A pdb=" N PHE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 435 removed outlier: 3.707A pdb=" N MET A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 741 removed outlier: 4.879A pdb=" N CYS A 736 " --> pdb=" O LYS A 732 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE A 737 " --> pdb=" O PHE A 733 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 739 " --> pdb=" O LYS A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 762 removed outlier: 3.625A pdb=" N ASP A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 796 removed outlier: 3.835A pdb=" N LYS A 794 " --> pdb=" O GLU A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 824 Processing helix chain 'A' and resid 833 through 848 removed outlier: 3.846A pdb=" N ARG A 838 " --> pdb=" O ARG A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 864 Processing helix chain 'A' and resid 866 through 888 removed outlier: 3.981A pdb=" N THR A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 895 removed outlier: 3.511A pdb=" N LYS A 893 " --> pdb=" O GLY A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 899 Processing helix chain 'A' and resid 912 through 926 Processing helix chain 'A' and resid 928 through 939 removed outlier: 3.831A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 972 removed outlier: 4.024A pdb=" N CYS A 944 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 957 " --> pdb=" O VAL A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1014 Processing helix chain 'A' and resid 1176 through 1189 removed outlier: 4.185A pdb=" N THR A1184 " --> pdb=" O ASN A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1208 Processing helix chain 'A' and resid 1209 through 1212 Processing helix chain 'A' and resid 1215 through 1218 Processing helix chain 'A' and resid 1219 through 1248 removed outlier: 4.624A pdb=" N LYS A1231 " --> pdb=" O GLU A1227 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A1232 " --> pdb=" O TYR A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1254 Processing helix chain 'A' and resid 1256 through 1279 Processing helix chain 'A' and resid 1283 through 1292 Processing helix chain 'A' and resid 1293 through 1301 Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1304 through 1316 Processing helix chain 'A' and resid 1317 through 1343 removed outlier: 4.492A pdb=" N ASN A1323 " --> pdb=" O PRO A1319 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N VAL A1324 " --> pdb=" O SER A1320 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1377 removed outlier: 3.832A pdb=" N VAL A1376 " --> pdb=" O ALA A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1405 Processing helix chain 'A' and resid 1407 through 1417 removed outlier: 3.907A pdb=" N ILE A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1432 No H-bonds generated for 'chain 'A' and resid 1430 through 1432' Processing helix chain 'A' and resid 1433 through 1444 removed outlier: 3.822A pdb=" N PHE A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1463 removed outlier: 3.628A pdb=" N ASN A1459 " --> pdb=" O VAL A1455 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN A1463 " --> pdb=" O ASN A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1490 removed outlier: 3.619A pdb=" N LYS A1480 " --> pdb=" O GLU A1476 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR A1481 " --> pdb=" O GLU A1477 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS A1487 " --> pdb=" O ASN A1483 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A1488 " --> pdb=" O ALA A1484 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY A1489 " --> pdb=" O MET A1485 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A1490 " --> pdb=" O LYS A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1512 removed outlier: 4.319A pdb=" N CYS A1507 " --> pdb=" O LYS A1503 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1534 Processing helix chain 'A' and resid 1540 through 1569 Processing helix chain 'A' and resid 1576 through 1602 Processing helix chain 'A' and resid 1605 through 1613 Processing helix chain 'A' and resid 1616 through 1622 removed outlier: 4.393A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1623 through 1625 No H-bonds generated for 'chain 'A' and resid 1623 through 1625' Processing helix chain 'A' and resid 1630 through 1666 Proline residue: A1642 - end of helix Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 4.292A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1708 removed outlier: 3.889A pdb=" N LEU A1703 " --> pdb=" O GLY A1699 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A1704 " --> pdb=" O TRP A1700 " (cutoff:3.500A) Proline residue: A1706 - end of helix Processing helix chain 'A' and resid 1732 through 1766 removed outlier: 3.795A pdb=" N ILE A1744 " --> pdb=" O PHE A1740 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 192 Processing helix chain 'C' and resid 118 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 91 removed outlier: 3.960A pdb=" N PHE A 98 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 274 through 277 Processing sheet with id=AA3, first strand: chain 'A' and resid 1349 through 1351 Processing sheet with id=AA4, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA5, first strand: chain 'B' and resid 77 through 80 removed outlier: 6.987A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU B 74 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 9.444A pdb=" N THR B 53 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 31 through 33 removed outlier: 4.266A pdb=" N GLU C 31 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR C 51 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.447A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU C 147 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL C 40 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU C 65 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLN C 82 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N TRP C 67 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE C 80 " --> pdb=" O TRP C 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 46 through 48 removed outlier: 3.741A pdb=" N LEU C 48 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL C 112 " --> pdb=" O LEU C 48 " (cutoff:3.500A) 762 hydrogen bonds defined for protein. 2175 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: 2.30 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2081 1.32 - 1.45: 3720 1.45 - 1.57: 8030 1.57 - 1.70: 38 1.70 - 1.82: 161 Bond restraints: 14030 Sorted by residual: bond pdb=" O33 LPE A2016 " pdb=" P LPE A2016 " ideal model delta sigma weight residual 1.673 1.605 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" O33 LPE A2014 " pdb=" P LPE A2014 " ideal model delta sigma weight residual 1.673 1.605 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O33 LPE A2017 " pdb=" P LPE A2017 " ideal model delta sigma weight residual 1.673 1.606 0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O33 LPE A2012 " pdb=" P LPE A2012 " ideal model delta sigma weight residual 1.673 1.606 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" O33 LPE A2022 " pdb=" P LPE A2022 " ideal model delta sigma weight residual 1.673 1.606 0.067 2.00e-02 2.50e+03 1.12e+01 ... (remaining 14025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 18258 1.92 - 3.85: 544 3.85 - 5.77: 103 5.77 - 7.69: 49 7.69 - 9.62: 9 Bond angle restraints: 18963 Sorted by residual: angle pdb=" N THR A 851 " pdb=" CA THR A 851 " pdb=" C THR A 851 " ideal model delta sigma weight residual 113.18 108.09 5.09 1.33e+00 5.65e-01 1.47e+01 angle pdb=" N GLU A 771 " pdb=" CA GLU A 771 " pdb=" C GLU A 771 " ideal model delta sigma weight residual 111.28 107.53 3.75 1.09e+00 8.42e-01 1.18e+01 angle pdb=" C2 LPE A2022 " pdb=" C3 LPE A2022 " pdb=" O3 LPE A2022 " ideal model delta sigma weight residual 103.57 113.19 -9.62 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C2 LPE A2016 " pdb=" C1 LPE A2016 " pdb=" O1 LPE A2016 " ideal model delta sigma weight residual 103.19 111.56 -8.37 3.00e+00 1.11e-01 7.79e+00 angle pdb=" CA SER A1742 " pdb=" C SER A1742 " pdb=" O SER A1742 " ideal model delta sigma weight residual 120.82 117.89 2.93 1.05e+00 9.07e-01 7.77e+00 ... (remaining 18958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.97: 8272 29.97 - 59.93: 663 59.93 - 89.90: 39 89.90 - 119.87: 26 119.87 - 149.83: 8 Dihedral angle restraints: 9008 sinusoidal: 4368 harmonic: 4640 Sorted by residual: dihedral pdb=" CB CYS A 315 " pdb=" SG CYS A 315 " pdb=" SG CYS A 330 " pdb=" CB CYS A 330 " ideal model delta sinusoidal sigma weight residual -86.00 -167.99 81.99 1 1.00e+01 1.00e-02 8.26e+01 dihedral pdb=" CB CYS A1715 " pdb=" SG CYS A1715 " pdb=" SG CYS A1730 " pdb=" CB CYS A1730 " ideal model delta sinusoidal sigma weight residual 93.00 144.92 -51.92 1 1.00e+01 1.00e-02 3.68e+01 dihedral pdb=" CA VAL A1512 " pdb=" C VAL A1512 " pdb=" N THR A1513 " pdb=" CA THR A1513 " ideal model delta harmonic sigma weight residual 180.00 155.28 24.72 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 9005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1806 0.053 - 0.106: 293 0.106 - 0.158: 41 0.158 - 0.211: 5 0.211 - 0.264: 2 Chirality restraints: 2147 Sorted by residual: chirality pdb=" C1 NAG A2002 " pdb=" ND2 ASN A1366 " pdb=" C2 NAG A2002 " pdb=" O5 NAG A2002 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB THR A 817 " pdb=" CA THR A 817 " pdb=" OG1 THR A 817 " pdb=" CG2 THR A 817 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C2 PCW A2027 " pdb=" C1 PCW A2027 " pdb=" C3 PCW A2027 " pdb=" O2 PCW A2027 " both_signs ideal model delta sigma weight residual False -2.32 -2.51 0.19 2.00e-01 2.50e+01 8.91e-01 ... (remaining 2144 not shown) Planarity restraints: 2234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 PCW A2027 " 0.017 2.00e-02 2.50e+03 3.15e-02 9.95e+00 pdb=" C19 PCW A2027 " -0.041 2.00e-02 2.50e+03 pdb=" C20 PCW A2027 " 0.041 2.00e-02 2.50e+03 pdb=" C21 PCW A2027 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 PCW A2018 " -0.012 2.00e-02 2.50e+03 2.25e-02 5.08e+00 pdb=" C39 PCW A2018 " 0.029 2.00e-02 2.50e+03 pdb=" C40 PCW A2018 " -0.029 2.00e-02 2.50e+03 pdb=" C41 PCW A2018 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A1641 " -0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO A1642 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A1642 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1642 " -0.032 5.00e-02 4.00e+02 ... (remaining 2231 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1008 2.73 - 3.28: 13916 3.28 - 3.82: 22034 3.82 - 4.36: 26413 4.36 - 4.90: 44838 Nonbonded interactions: 108209 Sorted by model distance: nonbonded pdb=" N GLN A1463 " pdb=" OE1 GLN A1463 " model vdw 2.193 3.120 nonbonded pdb=" OH TYR A1482 " pdb=" OE2 GLU A1761 " model vdw 2.203 3.040 nonbonded pdb=" OG SER A1320 " pdb=" OD1 ASN A1459 " model vdw 2.211 3.040 nonbonded pdb=" O LEU A1749 " pdb=" OD1 ASN A1753 " model vdw 2.268 3.040 nonbonded pdb=" OG SER A 321 " pdb=" O ALA A 374 " model vdw 2.278 3.040 ... (remaining 108204 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 'D' 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=0.00 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.390 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 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 : 0.006 0.068 14051 Z= 0.302 Angle : 0.847 9.618 19015 Z= 0.388 Chirality : 0.041 0.264 2147 Planarity : 0.004 0.070 2226 Dihedral : 20.156 149.834 5975 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.70 % Allowed : 34.37 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.72 (0.22), residues: 1564 helix: 1.55 (0.18), residues: 900 sheet: -0.65 (0.44), residues: 135 loop : -1.07 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 135 TYR 0.021 0.001 TYR A1481 PHE 0.032 0.001 PHE A 811 TRP 0.030 0.001 TRP A 151 HIS 0.010 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00606 (14030) covalent geometry : angle 0.84055 (18963) SS BOND : bond 0.00261 ( 11) SS BOND : angle 1.75782 ( 22) hydrogen bonds : bond 0.11333 ( 762) hydrogen bonds : angle 4.66673 ( 2175) link_BETA1-4 : bond 0.01623 ( 2) link_BETA1-4 : angle 4.07199 ( 6) link_NAG-ASN : bond 0.00225 ( 8) link_NAG-ASN : angle 1.71044 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 224 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1458 ASP cc_start: 0.7561 (p0) cc_final: 0.7156 (t70) outliers start: 10 outliers final: 8 residues processed: 233 average time/residue: 0.4860 time to fit residues: 126.2137 Evaluate side-chains 213 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 205 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain A residue 1571 HIS Chi-restraints excluded: chain B residue 114 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1401 GLN A1462 GLN A1571 HIS B 75 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.205737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.142280 restraints weight = 40318.145| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 3.81 r_work: 0.3606 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14051 Z= 0.144 Angle : 0.634 12.143 19015 Z= 0.315 Chirality : 0.042 0.215 2147 Planarity : 0.004 0.054 2226 Dihedral : 15.466 173.144 2951 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.94 % Allowed : 30.42 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.92 (0.22), residues: 1564 helix: 1.65 (0.18), residues: 902 sheet: -0.37 (0.47), residues: 121 loop : -0.91 (0.28), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 135 TYR 0.019 0.001 TYR A1481 PHE 0.015 0.001 PHE A 165 TRP 0.028 0.001 TRP A 151 HIS 0.008 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00328 (14030) covalent geometry : angle 0.62633 (18963) SS BOND : bond 0.00378 ( 11) SS BOND : angle 1.45276 ( 22) hydrogen bonds : bond 0.04194 ( 762) hydrogen bonds : angle 4.16019 ( 2175) link_BETA1-4 : bond 0.01343 ( 2) link_BETA1-4 : angle 3.24699 ( 6) link_NAG-ASN : bond 0.00287 ( 8) link_NAG-ASN : angle 2.02528 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 222 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.5888 (OUTLIER) cc_final: 0.5566 (tptt) REVERT: A 93 LYS cc_start: 0.7785 (tmmt) cc_final: 0.7561 (ttmt) REVERT: A 130 MET cc_start: 0.7362 (mmm) cc_final: 0.7108 (mmp) REVERT: A 166 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7871 (tm-30) REVERT: A 176 PHE cc_start: 0.8650 (t80) cc_final: 0.8438 (t80) REVERT: A 181 PHE cc_start: 0.7050 (OUTLIER) cc_final: 0.6536 (m-10) REVERT: A 1286 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8247 (mp) REVERT: B 29 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7341 (mp0) outliers start: 56 outliers final: 15 residues processed: 259 average time/residue: 0.4870 time to fit residues: 140.5802 Evaluate side-chains 228 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1286 ILE Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1571 HIS Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 163 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 13 optimal weight: 0.9980 chunk 134 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 128 optimal weight: 0.0970 chunk 46 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A1180 ASN A1462 GLN B 75 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.205809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.141185 restraints weight = 31556.592| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 3.40 r_work: 0.3625 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 14051 Z= 0.134 Angle : 0.631 16.274 19015 Z= 0.307 Chirality : 0.042 0.213 2147 Planarity : 0.003 0.055 2226 Dihedral : 14.365 172.801 2943 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.45 % Allowed : 30.92 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 1.01 (0.22), residues: 1564 helix: 1.72 (0.18), residues: 902 sheet: -0.32 (0.45), residues: 133 loop : -0.88 (0.28), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 838 TYR 0.020 0.001 TYR A 367 PHE 0.014 0.001 PHE A 811 TRP 0.029 0.001 TRP A 151 HIS 0.002 0.000 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00311 (14030) covalent geometry : angle 0.62486 (18963) SS BOND : bond 0.00364 ( 11) SS BOND : angle 1.32239 ( 22) hydrogen bonds : bond 0.03955 ( 762) hydrogen bonds : angle 4.05545 ( 2175) link_BETA1-4 : bond 0.01537 ( 2) link_BETA1-4 : angle 3.27271 ( 6) link_NAG-ASN : bond 0.00298 ( 8) link_NAG-ASN : angle 1.69249 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 215 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.5930 (OUTLIER) cc_final: 0.5598 (tppt) REVERT: A 93 LYS cc_start: 0.7827 (tmmt) cc_final: 0.7567 (ttmt) REVERT: A 99 ARG cc_start: 0.7709 (mtm-85) cc_final: 0.7508 (ttm-80) REVERT: A 133 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.6782 (mtm) REVERT: A 176 PHE cc_start: 0.8589 (t80) cc_final: 0.8305 (t80) REVERT: A 181 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6657 (m-10) REVERT: A 240 GLN cc_start: 0.7330 (mm-40) cc_final: 0.6726 (pt0) REVERT: A 358 MET cc_start: 0.7619 (tpt) cc_final: 0.7185 (tpt) REVERT: A 771 GLU cc_start: 0.6358 (pp20) cc_final: 0.6149 (pm20) REVERT: A 1412 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8217 (mtt) REVERT: A 1458 ASP cc_start: 0.8069 (t70) cc_final: 0.7760 (t0) REVERT: B 29 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: B 174 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8220 (tm) REVERT: B 178 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.6883 (mtt) REVERT: C 113 MET cc_start: 0.4453 (ppp) cc_final: 0.3175 (tpt) REVERT: C 130 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.5791 (tmm) outliers start: 49 outliers final: 21 residues processed: 244 average time/residue: 0.4820 time to fit residues: 131.7220 Evaluate side-chains 235 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 181 PHE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 895 CYS Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 130 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 116 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 153 optimal weight: 20.0000 chunk 2 optimal weight: 30.0000 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1753 ASN B 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.205003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.143388 restraints weight = 38712.852| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 4.09 r_work: 0.3596 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14051 Z= 0.140 Angle : 0.613 14.690 19015 Z= 0.302 Chirality : 0.042 0.230 2147 Planarity : 0.003 0.053 2226 Dihedral : 13.615 172.762 2941 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.30 % Allowed : 29.44 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.96 (0.22), residues: 1564 helix: 1.71 (0.18), residues: 899 sheet: -0.40 (0.45), residues: 133 loop : -0.94 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 838 TYR 0.019 0.001 TYR A 367 PHE 0.016 0.001 PHE A1661 TRP 0.031 0.001 TRP A 151 HIS 0.002 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00327 (14030) covalent geometry : angle 0.60608 (18963) SS BOND : bond 0.00364 ( 11) SS BOND : angle 1.44007 ( 22) hydrogen bonds : bond 0.03899 ( 762) hydrogen bonds : angle 3.98166 ( 2175) link_BETA1-4 : bond 0.01636 ( 2) link_BETA1-4 : angle 3.47232 ( 6) link_NAG-ASN : bond 0.00295 ( 8) link_NAG-ASN : angle 1.62179 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 216 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.5954 (OUTLIER) cc_final: 0.5522 (tptt) REVERT: A 93 LYS cc_start: 0.8256 (tmmt) cc_final: 0.8009 (ttmt) REVERT: A 99 ARG cc_start: 0.7564 (mtm-85) cc_final: 0.7347 (ttm-80) REVERT: A 152 THR cc_start: 0.8172 (p) cc_final: 0.7850 (t) REVERT: A 176 PHE cc_start: 0.8621 (t80) cc_final: 0.8406 (t80) REVERT: A 234 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7483 (mp) REVERT: A 240 GLN cc_start: 0.7268 (mm-40) cc_final: 0.6641 (pt0) REVERT: A 268 MET cc_start: 0.8255 (ttp) cc_final: 0.7941 (ttp) REVERT: A 358 MET cc_start: 0.7721 (tpt) cc_final: 0.7283 (tpt) REVERT: A 1474 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7711 (mtt) REVERT: A 1760 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8022 (mp) REVERT: B 29 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: B 174 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8161 (tm) REVERT: B 178 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7051 (mtt) REVERT: C 113 MET cc_start: 0.4112 (ppp) cc_final: 0.2946 (tpt) REVERT: C 130 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6034 (tmm) outliers start: 61 outliers final: 25 residues processed: 253 average time/residue: 0.4788 time to fit residues: 135.6121 Evaluate side-chains 238 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 824 PHE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 895 CYS Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1355 ASP Chi-restraints excluded: chain A residue 1474 MET Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 1760 LEU Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 130 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 96 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 83 optimal weight: 0.0980 chunk 62 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN B 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.205887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.149061 restraints weight = 24186.577| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.93 r_work: 0.3665 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14051 Z= 0.124 Angle : 0.604 15.817 19015 Z= 0.295 Chirality : 0.041 0.235 2147 Planarity : 0.003 0.052 2226 Dihedral : 13.274 171.703 2941 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.52 % Allowed : 30.56 % Favored : 65.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 1.03 (0.22), residues: 1564 helix: 1.78 (0.18), residues: 900 sheet: -0.37 (0.45), residues: 133 loop : -0.95 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 838 TYR 0.018 0.001 TYR A1481 PHE 0.030 0.001 PHE A 165 TRP 0.032 0.001 TRP A 151 HIS 0.002 0.000 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00285 (14030) covalent geometry : angle 0.59748 (18963) SS BOND : bond 0.00339 ( 11) SS BOND : angle 1.22041 ( 22) hydrogen bonds : bond 0.03718 ( 762) hydrogen bonds : angle 3.93350 ( 2175) link_BETA1-4 : bond 0.01581 ( 2) link_BETA1-4 : angle 3.39677 ( 6) link_NAG-ASN : bond 0.00287 ( 8) link_NAG-ASN : angle 1.65710 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.5954 (OUTLIER) cc_final: 0.5527 (tptt) REVERT: A 93 LYS cc_start: 0.8278 (tmmt) cc_final: 0.8027 (ttmt) REVERT: A 170 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7275 (mptm) REVERT: A 176 PHE cc_start: 0.8525 (t80) cc_final: 0.8313 (t80) REVERT: A 234 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7459 (mp) REVERT: A 240 GLN cc_start: 0.7286 (mm-40) cc_final: 0.6687 (pt0) REVERT: A 268 MET cc_start: 0.8178 (ttp) cc_final: 0.7873 (ttp) REVERT: A 307 GLU cc_start: 0.8341 (tp30) cc_final: 0.7242 (mp0) REVERT: A 358 MET cc_start: 0.7639 (tpt) cc_final: 0.7143 (tpt) REVERT: A 1323 ASN cc_start: 0.8295 (OUTLIER) cc_final: 0.8071 (t0) REVERT: A 1412 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8207 (mtt) REVERT: A 1474 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7718 (mtt) REVERT: B 29 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: B 174 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8211 (tm) REVERT: B 178 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7146 (mtt) REVERT: C 113 MET cc_start: 0.4035 (ppp) cc_final: 0.2919 (tpt) outliers start: 50 outliers final: 22 residues processed: 252 average time/residue: 0.4562 time to fit residues: 128.7831 Evaluate side-chains 240 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 824 PHE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 895 CYS Chi-restraints excluded: chain A residue 1323 ASN Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1474 MET Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 0.0370 chunk 152 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 89 optimal weight: 0.5980 chunk 146 optimal weight: 0.2980 chunk 91 optimal weight: 0.8980 chunk 134 optimal weight: 0.0470 chunk 35 optimal weight: 3.9990 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN B 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.207359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.144135 restraints weight = 36926.701| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 3.87 r_work: 0.3631 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14051 Z= 0.113 Angle : 0.604 15.844 19015 Z= 0.293 Chirality : 0.041 0.258 2147 Planarity : 0.003 0.051 2226 Dihedral : 12.904 171.643 2941 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.17 % Allowed : 30.99 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 1.13 (0.22), residues: 1564 helix: 1.89 (0.18), residues: 894 sheet: -0.33 (0.46), residues: 133 loop : -0.92 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 838 TYR 0.018 0.001 TYR A 367 PHE 0.019 0.001 PHE A1661 TRP 0.047 0.002 TRP A 730 HIS 0.001 0.000 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00252 (14030) covalent geometry : angle 0.59751 (18963) SS BOND : bond 0.00272 ( 11) SS BOND : angle 1.04345 ( 22) hydrogen bonds : bond 0.03516 ( 762) hydrogen bonds : angle 3.87392 ( 2175) link_BETA1-4 : bond 0.01527 ( 2) link_BETA1-4 : angle 3.29622 ( 6) link_NAG-ASN : bond 0.00275 ( 8) link_NAG-ASN : angle 1.67538 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.5870 (OUTLIER) cc_final: 0.5603 (tptt) REVERT: A 93 LYS cc_start: 0.8270 (tmmt) cc_final: 0.7977 (ttmt) REVERT: A 152 THR cc_start: 0.8172 (p) cc_final: 0.7848 (t) REVERT: A 176 PHE cc_start: 0.8559 (t80) cc_final: 0.8325 (t80) REVERT: A 234 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7447 (mp) REVERT: A 240 GLN cc_start: 0.7150 (mm-40) cc_final: 0.6537 (pt0) REVERT: A 296 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6603 (tm-30) REVERT: A 771 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.6234 (pp20) REVERT: A 1412 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8215 (mtt) REVERT: A 1474 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7766 (mtt) REVERT: A 1561 GLU cc_start: 0.8391 (pp20) cc_final: 0.8072 (pm20) REVERT: B 29 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: B 56 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8272 (mt-10) REVERT: B 174 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8141 (tm) REVERT: B 178 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7100 (mtt) REVERT: C 113 MET cc_start: 0.3882 (ppp) cc_final: 0.2848 (tpt) outliers start: 45 outliers final: 19 residues processed: 247 average time/residue: 0.4749 time to fit residues: 130.9833 Evaluate side-chains 236 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 895 CYS Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1474 MET Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 178 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 43 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN B 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.204246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.140989 restraints weight = 41121.655| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 3.85 r_work: 0.3583 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 14051 Z= 0.156 Angle : 0.637 16.565 19015 Z= 0.315 Chirality : 0.043 0.266 2147 Planarity : 0.004 0.052 2226 Dihedral : 12.983 171.088 2941 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.31 % Allowed : 31.13 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.93 (0.22), residues: 1564 helix: 1.71 (0.18), residues: 900 sheet: -0.46 (0.45), residues: 131 loop : -0.98 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 838 TYR 0.021 0.002 TYR A 367 PHE 0.017 0.001 PHE A1603 TRP 0.051 0.002 TRP A 730 HIS 0.003 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00371 (14030) covalent geometry : angle 0.62988 (18963) SS BOND : bond 0.00376 ( 11) SS BOND : angle 1.37582 ( 22) hydrogen bonds : bond 0.03898 ( 762) hydrogen bonds : angle 3.98667 ( 2175) link_BETA1-4 : bond 0.01625 ( 2) link_BETA1-4 : angle 3.45394 ( 6) link_NAG-ASN : bond 0.00247 ( 8) link_NAG-ASN : angle 1.71697 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 214 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.5809 (OUTLIER) cc_final: 0.5505 (tptt) REVERT: A 93 LYS cc_start: 0.8273 (tmmt) cc_final: 0.7966 (ttmt) REVERT: A 234 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7522 (mp) REVERT: A 240 GLN cc_start: 0.7168 (mm-40) cc_final: 0.6556 (pt0) REVERT: A 296 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6678 (tm-30) REVERT: A 358 MET cc_start: 0.7712 (tpt) cc_final: 0.7270 (tpt) REVERT: A 771 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.6170 (pp20) REVERT: A 835 ARG cc_start: 0.8318 (mtm180) cc_final: 0.8090 (mtm180) REVERT: A 1412 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8230 (mtt) REVERT: A 1730 CYS cc_start: 0.6422 (p) cc_final: 0.6150 (m) REVERT: B 29 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: C 113 MET cc_start: 0.3832 (ppp) cc_final: 0.2801 (tpt) outliers start: 47 outliers final: 26 residues processed: 238 average time/residue: 0.4727 time to fit residues: 125.8926 Evaluate side-chains 240 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 824 PHE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 895 CYS Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 150 optimal weight: 0.0070 chunk 42 optimal weight: 0.8980 chunk 132 optimal weight: 0.0030 chunk 126 optimal weight: 0.9980 chunk 139 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 155 optimal weight: 0.0020 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.2416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN B 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.208243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.147534 restraints weight = 33577.881| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 3.57 r_work: 0.3661 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 14051 Z= 0.112 Angle : 0.603 16.393 19015 Z= 0.299 Chirality : 0.041 0.258 2147 Planarity : 0.003 0.052 2226 Dihedral : 12.551 170.657 2941 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.61 % Allowed : 31.97 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 1.15 (0.22), residues: 1564 helix: 1.92 (0.18), residues: 895 sheet: -0.42 (0.45), residues: 133 loop : -0.90 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 838 TYR 0.016 0.001 TYR A1481 PHE 0.019 0.001 PHE A1661 TRP 0.038 0.001 TRP A 151 HIS 0.001 0.000 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00249 (14030) covalent geometry : angle 0.59769 (18963) SS BOND : bond 0.00259 ( 11) SS BOND : angle 0.98677 ( 22) hydrogen bonds : bond 0.03447 ( 762) hydrogen bonds : angle 3.90074 ( 2175) link_BETA1-4 : bond 0.01496 ( 2) link_BETA1-4 : angle 3.18097 ( 6) link_NAG-ASN : bond 0.00275 ( 8) link_NAG-ASN : angle 1.67639 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.5856 (OUTLIER) cc_final: 0.5533 (tptt) REVERT: A 93 LYS cc_start: 0.8262 (tmmt) cc_final: 0.7982 (ttmt) REVERT: A 234 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7368 (mp) REVERT: A 240 GLN cc_start: 0.7204 (mm-40) cc_final: 0.6615 (pt0) REVERT: A 771 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.6168 (pp20) REVERT: A 835 ARG cc_start: 0.8303 (mtm180) cc_final: 0.8082 (mtm180) REVERT: A 1412 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8235 (mtt) REVERT: A 1561 GLU cc_start: 0.8376 (pp20) cc_final: 0.8005 (pm20) REVERT: A 1730 CYS cc_start: 0.5974 (p) cc_final: 0.5773 (m) REVERT: B 29 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: B 56 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8229 (mt-10) REVERT: B 151 ASN cc_start: 0.8619 (m-40) cc_final: 0.8234 (m-40) REVERT: B 174 LEU cc_start: 0.8452 (tp) cc_final: 0.8027 (tm) REVERT: B 178 MET cc_start: 0.7716 (mtm) cc_final: 0.7005 (mpp) REVERT: C 85 MET cc_start: 0.7656 (tpt) cc_final: 0.6270 (tpp) REVERT: C 113 MET cc_start: 0.3819 (ppp) cc_final: 0.2808 (tpt) outliers start: 37 outliers final: 21 residues processed: 236 average time/residue: 0.4669 time to fit residues: 123.6475 Evaluate side-chains 236 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 895 CYS Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 109 optimal weight: 0.7980 chunk 129 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN B 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.209985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.150562 restraints weight = 34648.757| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 3.40 r_work: 0.3787 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14051 Z= 0.132 Angle : 0.624 16.869 19015 Z= 0.307 Chirality : 0.042 0.272 2147 Planarity : 0.003 0.053 2226 Dihedral : 12.525 170.844 2941 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.61 % Allowed : 32.04 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 1.07 (0.22), residues: 1564 helix: 1.84 (0.18), residues: 896 sheet: -0.40 (0.45), residues: 131 loop : -0.93 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 838 TYR 0.022 0.001 TYR A1572 PHE 0.019 0.001 PHE A 159 TRP 0.037 0.001 TRP A 151 HIS 0.002 0.000 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00307 (14030) covalent geometry : angle 0.61778 (18963) SS BOND : bond 0.00320 ( 11) SS BOND : angle 1.15385 ( 22) hydrogen bonds : bond 0.03607 ( 762) hydrogen bonds : angle 3.92660 ( 2175) link_BETA1-4 : bond 0.01538 ( 2) link_BETA1-4 : angle 3.27732 ( 6) link_NAG-ASN : bond 0.00256 ( 8) link_NAG-ASN : angle 1.64566 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.5690 (OUTLIER) cc_final: 0.5440 (tptt) REVERT: A 152 THR cc_start: 0.8168 (p) cc_final: 0.7862 (t) REVERT: A 234 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7263 (mp) REVERT: A 240 GLN cc_start: 0.7071 (mm-40) cc_final: 0.6448 (pt0) REVERT: A 296 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6537 (tm-30) REVERT: A 358 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.7006 (tpt) REVERT: A 771 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.6102 (pp20) REVERT: A 835 ARG cc_start: 0.8183 (mtm180) cc_final: 0.7935 (mtm180) REVERT: A 1412 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8097 (mtt) REVERT: A 1462 GLN cc_start: 0.7351 (pt0) cc_final: 0.7050 (pm20) REVERT: A 1730 CYS cc_start: 0.5946 (p) cc_final: 0.5721 (m) REVERT: B 29 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: B 56 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8162 (mt-10) REVERT: B 151 ASN cc_start: 0.8608 (m-40) cc_final: 0.8203 (m-40) REVERT: B 174 LEU cc_start: 0.8343 (tp) cc_final: 0.7860 (tm) REVERT: B 178 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.6710 (mpp) REVERT: C 85 MET cc_start: 0.7624 (tpt) cc_final: 0.6193 (tpp) REVERT: C 113 MET cc_start: 0.3806 (ppp) cc_final: 0.2802 (tpt) outliers start: 37 outliers final: 24 residues processed: 233 average time/residue: 0.4430 time to fit residues: 115.4692 Evaluate side-chains 242 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 739 PHE Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 771 GLU Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 895 CYS Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 152 optimal weight: 0.0670 chunk 102 optimal weight: 0.6980 chunk 139 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 124 optimal weight: 0.0470 chunk 53 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN B 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.210785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.152378 restraints weight = 28071.985| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 3.12 r_work: 0.3821 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3809 r_free = 0.3809 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3809 r_free = 0.3809 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14051 Z= 0.120 Angle : 0.624 16.830 19015 Z= 0.308 Chirality : 0.042 0.284 2147 Planarity : 0.003 0.052 2226 Dihedral : 12.372 170.117 2941 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.32 % Allowed : 32.54 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 1.12 (0.22), residues: 1564 helix: 1.87 (0.18), residues: 898 sheet: -0.38 (0.45), residues: 131 loop : -0.91 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 838 TYR 0.019 0.001 TYR A 367 PHE 0.018 0.001 PHE A1603 TRP 0.039 0.001 TRP A 151 HIS 0.002 0.000 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00277 (14030) covalent geometry : angle 0.61887 (18963) SS BOND : bond 0.00277 ( 11) SS BOND : angle 1.04759 ( 22) hydrogen bonds : bond 0.03520 ( 762) hydrogen bonds : angle 3.91611 ( 2175) link_BETA1-4 : bond 0.01531 ( 2) link_BETA1-4 : angle 3.21949 ( 6) link_NAG-ASN : bond 0.00258 ( 8) link_NAG-ASN : angle 1.61048 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LYS cc_start: 0.5734 (OUTLIER) cc_final: 0.5426 (tptt) REVERT: A 152 THR cc_start: 0.8164 (p) cc_final: 0.7847 (t) REVERT: A 176 PHE cc_start: 0.8499 (t80) cc_final: 0.8215 (t80) REVERT: A 234 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7221 (mp) REVERT: A 240 GLN cc_start: 0.7044 (mm-40) cc_final: 0.6424 (pt0) REVERT: A 296 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6488 (tm-30) REVERT: A 358 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6958 (tpt) REVERT: A 835 ARG cc_start: 0.8162 (mtm180) cc_final: 0.7926 (mtm180) REVERT: A 1412 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8035 (mtt) REVERT: A 1730 CYS cc_start: 0.5820 (p) cc_final: 0.5578 (m) REVERT: B 29 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: B 56 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8144 (mt-10) REVERT: B 151 ASN cc_start: 0.8577 (m-40) cc_final: 0.8191 (m-40) REVERT: B 174 LEU cc_start: 0.8331 (tp) cc_final: 0.8025 (tm) REVERT: B 178 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7395 (mtm) REVERT: B 184 LYS cc_start: 0.7693 (tptp) cc_final: 0.7490 (tptt) REVERT: C 85 MET cc_start: 0.7713 (tpt) cc_final: 0.6241 (tpp) REVERT: C 113 MET cc_start: 0.3809 (ppp) cc_final: 0.2797 (tpt) outliers start: 33 outliers final: 23 residues processed: 231 average time/residue: 0.4704 time to fit residues: 121.6465 Evaluate side-chains 237 residues out of total 1412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 895 CYS Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1412 MET Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1602 TYR Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 152 ARG Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 153 optimal weight: 0.0970 chunk 37 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 58 optimal weight: 0.1980 chunk 78 optimal weight: 0.2980 chunk 136 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN B 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.211128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.152102 restraints weight = 32326.311| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 3.31 r_work: 0.3820 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14051 Z= 0.119 Angle : 0.630 16.771 19015 Z= 0.310 Chirality : 0.042 0.286 2147 Planarity : 0.003 0.054 2226 Dihedral : 12.310 169.933 2941 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.46 % Allowed : 32.54 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 1.15 (0.22), residues: 1564 helix: 1.90 (0.18), residues: 898 sheet: -0.37 (0.46), residues: 131 loop : -0.89 (0.28), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 838 TYR 0.024 0.001 TYR A1572 PHE 0.018 0.001 PHE A1603 TRP 0.038 0.001 TRP A 151 HIS 0.001 0.000 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00271 (14030) covalent geometry : angle 0.62434 (18963) SS BOND : bond 0.00275 ( 11) SS BOND : angle 1.02396 ( 22) hydrogen bonds : bond 0.03503 ( 762) hydrogen bonds : angle 3.90588 ( 2175) link_BETA1-4 : bond 0.01500 ( 2) link_BETA1-4 : angle 3.20003 ( 6) link_NAG-ASN : bond 0.00260 ( 8) link_NAG-ASN : angle 1.59515 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6287.26 seconds wall clock time: 107 minutes 34.60 seconds (6454.60 seconds total)