Starting phenix.real_space_refine on Wed Mar 4 23:47:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6um1_20815/03_2026/6um1_20815.cif Found real_map, /net/cci-nas-00/data/ceres_data/6um1_20815/03_2026/6um1_20815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6um1_20815/03_2026/6um1_20815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6um1_20815/03_2026/6um1_20815.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6um1_20815/03_2026/6um1_20815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6um1_20815/03_2026/6um1_20815.map" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 136 5.16 5 C 10693 2.51 5 N 2923 2.21 5 O 3382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17134 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 17025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2208, 17025 Classifications: {'peptide': 2208} Link IDs: {'PTRANS': 110, 'TRANS': 2097} Chain breaks: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.20, per 1000 atoms: 0.19 Number of scatterers: 17134 At special positions: 0 Unit cell: (174, 108, 146, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 136 16.00 O 3382 8.00 N 2923 7.00 C 10693 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=59, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 92 " distance=2.04 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 167 " distance=2.04 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 241 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 375 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 391 " distance=2.04 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 463 " distance=2.05 Simple disulfide: pdb=" SG CYS A 443 " - pdb=" SG CYS A 475 " distance=2.04 Simple disulfide: pdb=" SG CYS A 484 " - pdb=" SG CYS A 528 " distance=2.01 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 547 " distance=2.03 Simple disulfide: pdb=" SG CYS A 581 " - pdb=" SG CYS A 614 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 626 " distance=2.04 Simple disulfide: pdb=" SG CYS A 636 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 680 " - pdb=" SG CYS A 687 " distance=2.03 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 768 " distance=2.03 Simple disulfide: pdb=" SG CYS A 775 " - pdb=" SG CYS A 822 " distance=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS A 838 " distance=2.05 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS A 918 " distance=2.03 Simple disulfide: pdb=" SG CYS A 901 " - pdb=" SG CYS A 930 " distance=2.04 Simple disulfide: pdb=" SG CYS A 942 " - pdb=" SG CYS A 978 " distance=2.03 Simple disulfide: pdb=" SG CYS A 984 " - pdb=" SG CYS A 995 " distance=2.03 Simple disulfide: pdb=" SG CYS A1051 " - pdb=" SG CYS A1086 " distance=2.03 Simple disulfide: pdb=" SG CYS A1093 " - pdb=" SG CYS A1134 " distance=2.02 Simple disulfide: pdb=" SG CYS A1143 " - pdb=" SG CYS A1151 " distance=2.04 Simple disulfide: pdb=" SG CYS A1186 " - pdb=" SG CYS A1214 " distance=2.03 Simple disulfide: pdb=" SG CYS A1199 " - pdb=" SG CYS A1226 " distance=2.04 Simple disulfide: pdb=" SG CYS A1236 " - pdb=" SG CYS A1271 " distance=2.04 Simple disulfide: pdb=" SG CYS A1279 " - pdb=" SG CYS A1291 " distance=2.00 Simple disulfide: pdb=" SG CYS A1328 " - pdb=" SG CYS A1358 " distance=2.01 Simple disulfide: pdb=" SG CYS A1342 " - pdb=" SG CYS A1370 " distance=2.05 Simple disulfide: pdb=" SG CYS A1378 " - pdb=" SG CYS A1417 " distance=2.03 Simple disulfide: pdb=" SG CYS A1429 " - pdb=" SG CYS A1436 " distance=2.02 Simple disulfide: pdb=" SG CYS A1470 " - pdb=" SG CYS A1503 " distance=2.03 Simple disulfide: pdb=" SG CYS A1485 " - pdb=" SG CYS A1515 " distance=2.04 Simple disulfide: pdb=" SG CYS A1525 " - pdb=" SG CYS A1562 " distance=2.03 Simple disulfide: pdb=" SG CYS A1568 " - pdb=" SG CYS A1575 " distance=2.03 Simple disulfide: pdb=" SG CYS A1607 " - pdb=" SG CYS A1643 " distance=2.02 Simple disulfide: pdb=" SG CYS A1623 " - pdb=" SG CYS A1655 " distance=2.03 Simple disulfide: pdb=" SG CYS A1661 " - pdb=" SG CYS A1704 " distance=2.03 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1722 " distance=2.04 Simple disulfide: pdb=" SG CYS A1759 " - pdb=" SG CYS A1792 " distance=2.04 Simple disulfide: pdb=" SG CYS A1775 " - pdb=" SG CYS A1804 " distance=2.03 Simple disulfide: pdb=" SG CYS A1813 " - pdb=" SG CYS A1848 " distance=2.04 Simple disulfide: pdb=" SG CYS A1859 " - pdb=" SG CYS A1865 " distance=2.03 Simple disulfide: pdb=" SG CYS A1902 " - pdb=" SG CYS A1984 " distance=2.04 Simple disulfide: pdb=" SG CYS A1912 " - pdb=" SG CYS A1936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1926 " - pdb=" SG CYS A1951 " distance=2.04 Simple disulfide: pdb=" SG CYS A1966 " - pdb=" SG CYS A1996 " distance=2.04 Simple disulfide: pdb=" SG CYS A2003 " - pdb=" SG CYS A2038 " distance=2.02 Simple disulfide: pdb=" SG CYS A2048 " - pdb=" SG CYS A2055 " distance=2.03 Simple disulfide: pdb=" SG CYS A2091 " - pdb=" SG CYS A2122 " distance=2.03 Simple disulfide: pdb=" SG CYS A2105 " - pdb=" SG CYS A2134 " distance=2.03 Simple disulfide: pdb=" SG CYS A2197 " - pdb=" SG CYS A2203 " distance=2.03 Simple disulfide: pdb=" SG CYS A2241 " - pdb=" SG CYS A2275 " distance=2.03 Simple disulfide: pdb=" SG CYS A2257 " - pdb=" SG CYS A2287 " distance=2.04 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=2, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A2501 " - " ASN A 120 " " NAG A2507 " - " ASN A1030 " " NAG B 1 " - " ASN A 444 " " NAG C 1 " - " ASN A 590 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 747.8 milliseconds 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4076 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 50 sheets defined 2.5% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 193 through 196 Processing helix chain 'A' and resid 321 through 324 Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 447 through 452 Processing helix chain 'A' and resid 650 through 653 Processing helix chain 'A' and resid 869 through 871 No H-bonds generated for 'chain 'A' and resid 869 through 871' Processing helix chain 'A' and resid 956 through 959 Processing helix chain 'A' and resid 1106 through 1110 Processing helix chain 'A' and resid 1249 through 1253 Processing helix chain 'A' and resid 1391 through 1394 Processing helix chain 'A' and resid 1539 through 1542 Processing helix chain 'A' and resid 1673 through 1676 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 63 Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 112 removed outlier: 4.212A pdb=" N THR A 121 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE A 132 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 151 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU A 160 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N PHE A 149 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA4, first strand: chain 'A' and resid 202 through 204 removed outlier: 4.660A pdb=" N LEU A 213 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 271 removed outlier: 6.115A pdb=" N ALA A 287 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE A 316 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR A 289 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TRP A 318 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N THR A 291 " --> pdb=" O TRP A 318 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU A 315 " --> pdb=" O THR A 307 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 328 through 331 removed outlier: 4.570A pdb=" N LEU A 419 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 437 " --> pdb=" O TYR A 423 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR A 465 " --> pdb=" O MET A 436 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 363 removed outlier: 6.218A pdb=" N VAL A 390 " --> pdb=" O ALA A 404 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 485 through 488 Processing sheet with id=AA9, first strand: chain 'A' and resid 511 through 512 removed outlier: 7.454A pdb=" N VAL A 511 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 522 through 525 Processing sheet with id=AB2, first strand: chain 'A' and resid 631 through 633 removed outlier: 6.008A pdb=" N LEU A 734 " --> pdb=" O PHE A 760 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N TRP A 762 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N THR A 736 " --> pdb=" O TRP A 762 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR A 764 " --> pdb=" O THR A 736 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU A 738 " --> pdb=" O THR A 764 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 637 through 639 Processing sheet with id=AB4, first strand: chain 'A' and resid 660 through 661 Processing sheet with id=AB5, first strand: chain 'A' and resid 777 through 778 Processing sheet with id=AB6, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AB7, first strand: chain 'A' and resid 866 through 867 removed outlier: 6.765A pdb=" N THR A 894 " --> pdb=" O VAL A 920 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 866 through 867 removed outlier: 7.765A pdb=" N TRP A 924 " --> pdb=" O ARG A 896 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N HIS A 898 " --> pdb=" O TRP A 924 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N THR A 926 " --> pdb=" O HIS A 898 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL A 900 " --> pdb=" O THR A 926 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 943 through 945 Processing sheet with id=AC1, first strand: chain 'A' and resid 964 through 966 Processing sheet with id=AC2, first strand: chain 'A' and resid 1015 through 1016 Processing sheet with id=AC3, first strand: chain 'A' and resid 1019 through 1021 removed outlier: 4.038A pdb=" N ILE A1027 " --> pdb=" O PHE A1049 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N PHE A1080 " --> pdb=" O ILE A1046 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ARG A1048 " --> pdb=" O PHE A1080 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1065 through 1067 Processing sheet with id=AC5, first strand: chain 'A' and resid 1094 through 1095 Processing sheet with id=AC6, first strand: chain 'A' and resid 1128 through 1129 Processing sheet with id=AC7, first strand: chain 'A' and resid 1169 through 1170 removed outlier: 6.772A pdb=" N GLU A1215 " --> pdb=" O GLN A1211 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLN A1211 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL A1217 " --> pdb=" O GLN A1209 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1257 through 1260 Processing sheet with id=AC9, first strand: chain 'A' and resid 1311 through 1314 removed outlier: 7.068A pdb=" N SER A1335 " --> pdb=" O TYR A1360 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N PHE A1362 " --> pdb=" O SER A1335 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR A1337 " --> pdb=" O PHE A1362 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N TRP A1364 " --> pdb=" O THR A1337 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE A1339 " --> pdb=" O TRP A1364 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR A1366 " --> pdb=" O PHE A1339 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N TYR A1341 " --> pdb=" O THR A1366 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU A1361 " --> pdb=" O LEU A1352 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ARG A1365 " --> pdb=" O ALA A1348 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ALA A1348 " --> pdb=" O ARG A1365 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1379 through 1381 removed outlier: 3.505A pdb=" N PHE A1380 " --> pdb=" O TYR A1388 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1400 through 1401 removed outlier: 6.057A pdb=" N VAL A1435 " --> pdb=" O LEU A1446 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 1400 through 1401 removed outlier: 6.057A pdb=" N VAL A1435 " --> pdb=" O LEU A1446 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR A1460 " --> pdb=" O PHE A1483 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N GLU A1504 " --> pdb=" O ALA A1499 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ALA A1499 " --> pdb=" O GLU A1504 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR A1506 " --> pdb=" O ILE A1497 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1520 through 1522 removed outlier: 3.607A pdb=" N ASN A1520 " --> pdb=" O TYR A1592 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A1647 " --> pdb=" O VAL A1618 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A1637 " --> pdb=" O PHE A1646 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 1520 through 1522 removed outlier: 3.607A pdb=" N ASN A1520 " --> pdb=" O TYR A1592 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N THR A1651 " --> pdb=" O SER A1620 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL A1622 " --> pdb=" O THR A1651 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 1526 through 1527 Processing sheet with id=AD7, first strand: chain 'A' and resid 1547 through 1550 Processing sheet with id=AD8, first strand: chain 'A' and resid 1662 through 1665 removed outlier: 3.542A pdb=" N ASN A1665 " --> pdb=" O SER A1668 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 1682 through 1683 removed outlier: 3.950A pdb=" N ILE A1731 " --> pdb=" O LYS A1723 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 1735 through 1736 Processing sheet with id=AE2, first strand: chain 'A' and resid 1735 through 1736 removed outlier: 7.138A pdb=" N THR A1768 " --> pdb=" O PHE A1794 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N PHE A1796 " --> pdb=" O THR A1768 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU A1770 " --> pdb=" O PHE A1796 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TRP A1798 " --> pdb=" O LEU A1770 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N THR A1772 " --> pdb=" O TRP A1798 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR A1800 " --> pdb=" O THR A1772 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N HIS A1774 " --> pdb=" O THR A1800 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 1834 through 1837 removed outlier: 7.260A pdb=" N GLY A1876 " --> pdb=" O ALA A1863 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 1885 through 1886 removed outlier: 3.794A pdb=" N ALA A1891 " --> pdb=" O ARG A1886 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU A1985 " --> pdb=" O GLU A1980 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU A1980 " --> pdb=" O GLU A1985 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR A1987 " --> pdb=" O PHE A1978 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 1916 through 1918 removed outlier: 3.538A pdb=" N PHE A1916 " --> pdb=" O TYR A1923 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 1935 through 1937 Processing sheet with id=AE7, first strand: chain 'A' and resid 2004 through 2006 removed outlier: 3.556A pdb=" N PHE A2005 " --> pdb=" O TYR A2012 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 2055 through 2057 Processing sheet with id=AE9, first strand: chain 'A' and resid 2074 through 2077 Processing sheet with id=AF1, first strand: chain 'A' and resid 2104 through 2105 removed outlier: 3.522A pdb=" N SER A2130 " --> pdb=" O THR A2104 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N HIS A2125 " --> pdb=" O THR A2115 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ASP A2129 " --> pdb=" O ARG A2111 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ARG A2111 " --> pdb=" O ASP A2129 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 2149 through 2150 removed outlier: 3.934A pdb=" N ARG A2155 " --> pdb=" O ASN A2150 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 2173 through 2175 removed outlier: 3.905A pdb=" N THR A2175 " --> pdb=" O TYR A2182 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR A2182 " --> pdb=" O THR A2175 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 2200 through 2202 removed outlier: 6.757A pdb=" N GLY A2217 " --> pdb=" O SER A2201 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 2222 through 2223 removed outlier: 6.188A pdb=" N THR A2252 " --> pdb=" O PHE A2279 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TRP A2281 " --> pdb=" O THR A2252 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N PHE A2254 " --> pdb=" O TRP A2281 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A2276 " --> pdb=" O THR A2272 " (cutoff:3.500A) 359 hydrogen bonds defined for protein. 837 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: 5.64 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3346 1.33 - 1.45: 4356 1.45 - 1.57: 9669 1.57 - 1.70: 0 1.70 - 1.82: 153 Bond restraints: 17524 Sorted by residual: bond pdb=" N ASP A1097 " pdb=" CA ASP A1097 " ideal model delta sigma weight residual 1.455 1.490 -0.035 7.00e-03 2.04e+04 2.46e+01 bond pdb=" N ILE A2265 " pdb=" CA ILE A2265 " ideal model delta sigma weight residual 1.456 1.496 -0.040 8.60e-03 1.35e+04 2.20e+01 bond pdb=" N ILE A2162 " pdb=" CA ILE A2162 " ideal model delta sigma weight residual 1.456 1.500 -0.043 9.50e-03 1.11e+04 2.08e+01 bond pdb=" N VAL A1331 " pdb=" CA VAL A1331 " ideal model delta sigma weight residual 1.458 1.498 -0.040 9.00e-03 1.23e+04 1.98e+01 bond pdb=" N ASP A1240 " pdb=" CA ASP A1240 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 1.97e+01 ... (remaining 17519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.14: 23250 4.14 - 8.28: 521 8.28 - 12.42: 18 12.42 - 16.56: 4 16.56 - 20.70: 3 Bond angle restraints: 23796 Sorted by residual: angle pdb=" C HIS A1037 " pdb=" N PRO A1038 " pdb=" CA PRO A1038 " ideal model delta sigma weight residual 119.84 133.98 -14.14 1.25e+00 6.40e-01 1.28e+02 angle pdb=" C ASP A 656 " pdb=" CA ASP A 656 " pdb=" CB ASP A 656 " ideal model delta sigma weight residual 109.55 92.90 16.65 1.68e+00 3.54e-01 9.82e+01 angle pdb=" N GLY A1425 " pdb=" CA GLY A1425 " pdb=" C GLY A1425 " ideal model delta sigma weight residual 113.18 92.48 20.70 2.37e+00 1.78e-01 7.63e+01 angle pdb=" N GLN A1423 " pdb=" CA GLN A1423 " pdb=" C GLN A1423 " ideal model delta sigma weight residual 107.73 95.01 12.72 1.80e+00 3.09e-01 5.00e+01 angle pdb=" C GLN A 515 " pdb=" N ARG A 516 " pdb=" CA ARG A 516 " ideal model delta sigma weight residual 120.38 130.70 -10.32 1.46e+00 4.69e-01 5.00e+01 ... (remaining 23791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 9950 24.08 - 48.16: 687 48.16 - 72.24: 75 72.24 - 96.33: 13 96.33 - 120.41: 8 Dihedral angle restraints: 10733 sinusoidal: 4361 harmonic: 6372 Sorted by residual: dihedral pdb=" CA PHE A1914 " pdb=" C PHE A1914 " pdb=" N PRO A1915 " pdb=" CA PRO A1915 " ideal model delta harmonic sigma weight residual -180.00 -70.55 -109.45 0 5.00e+00 4.00e-02 4.79e+02 dihedral pdb=" CB CYS A 57 " pdb=" SG CYS A 57 " pdb=" SG CYS A 77 " pdb=" CB CYS A 77 " ideal model delta sinusoidal sigma weight residual 93.00 -176.91 -90.09 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CB CYS A 334 " pdb=" SG CYS A 334 " pdb=" SG CYS A 375 " pdb=" CB CYS A 375 " ideal model delta sinusoidal sigma weight residual 93.00 -177.48 -89.52 1 1.00e+01 1.00e-02 9.52e+01 ... (remaining 10730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 2373 0.143 - 0.286: 257 0.286 - 0.429: 6 0.429 - 0.571: 2 0.571 - 0.714: 1 Chirality restraints: 2639 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.51e+01 chirality pdb=" C1 NAG A2501 " pdb=" ND2 ASN A 120 " pdb=" C2 NAG A2501 " pdb=" O5 NAG A2501 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" CA ARG A 332 " pdb=" N ARG A 332 " pdb=" C ARG A 332 " pdb=" CB ARG A 332 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.61e+00 ... (remaining 2636 not shown) Planarity restraints: 3110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 120 " -0.063 2.00e-02 2.50e+03 9.29e-02 1.08e+02 pdb=" CG ASN A 120 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 120 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 120 " 0.168 2.00e-02 2.50e+03 pdb=" C1 NAG A2501 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A1037 " -0.032 2.00e-02 2.50e+03 6.43e-02 4.13e+01 pdb=" C HIS A1037 " 0.111 2.00e-02 2.50e+03 pdb=" O HIS A1037 " -0.043 2.00e-02 2.50e+03 pdb=" N PRO A1038 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A1037 " 0.074 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO A1038 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO A1038 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A1038 " 0.048 5.00e-02 4.00e+02 ... (remaining 3107 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 146 2.59 - 3.17: 13295 3.17 - 3.75: 25691 3.75 - 4.32: 35514 4.32 - 4.90: 58759 Nonbonded interactions: 133405 Sorted by model distance: nonbonded pdb=" OG SER A2053 " pdb=" O GLY A2067 " model vdw 2.014 3.040 nonbonded pdb=" O GLY A 274 " pdb=" NE2 GLN A 277 " model vdw 2.136 3.120 nonbonded pdb=" N GLY A1425 " pdb=" O GLY A1425 " model vdw 2.204 2.496 nonbonded pdb=" O TYR A 717 " pdb=" O THR A 733 " model vdw 2.229 3.040 nonbonded pdb=" OD1 ASN A1321 " pdb=" C1 NAG A2508 " model vdw 2.252 3.470 ... (remaining 133400 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.680 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 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 : 0.014 0.127 17592 Z= 1.059 Angle : 1.841 28.915 23935 Z= 1.265 Chirality : 0.091 0.714 2639 Planarity : 0.006 0.110 3106 Dihedral : 15.713 120.408 6480 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.91 % Favored : 92.86 % Rotamer: Outliers : 0.84 % Allowed : 8.61 % Favored : 90.55 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.81 % 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: -4.82 (0.14), residues: 2200 helix: -4.65 (1.01), residues: 13 sheet: -3.48 (0.17), residues: 532 loop : -3.36 (0.12), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A1041 TYR 0.035 0.003 TYR A1373 PHE 0.037 0.003 PHE A1914 TRP 0.029 0.003 TRP A 924 HIS 0.010 0.002 HIS A 501 Details of bonding type rmsd covalent geometry : bond 0.01398 (17524) covalent geometry : angle 1.82881 (23796) SS BOND : bond 0.00876 ( 59) SS BOND : angle 1.94542 ( 118) hydrogen bonds : bond 0.28728 ( 329) hydrogen bonds : angle 12.44573 ( 837) Misc. bond : bond 0.08958 ( 2) link_BETA1-4 : bond 0.00557 ( 3) link_BETA1-4 : angle 3.08215 ( 9) link_NAG-ASN : bond 0.05879 ( 4) link_NAG-ASN : angle 9.09856 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 277 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ILE cc_start: 0.8422 (pt) cc_final: 0.8186 (pt) REVERT: A 787 ASP cc_start: 0.6535 (t70) cc_final: 0.6330 (p0) REVERT: A 1423 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7021 (mm-40) REVERT: A 2241 CYS cc_start: -0.1611 (OUTLIER) cc_final: -0.2033 (t) outliers start: 16 outliers final: 6 residues processed: 293 average time/residue: 0.1377 time to fit residues: 60.3103 Evaluate side-chains 180 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1423 GLN Chi-restraints excluded: chain A residue 1426 SER Chi-restraints excluded: chain A residue 1427 ASP Chi-restraints excluded: chain A residue 2241 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 127 GLN A 193 ASN A 311 ASN A 325 HIS ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 GLN A 857 ASN ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN A1039 ASN ** A1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1567 ASN A1631 ASN A1841 HIS A1887 HIS A2064 GLN A2145 ASN A2153 ASN A2227 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.190904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.155310 restraints weight = 22936.998| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.46 r_work: 0.3664 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 17592 Z= 0.177 Angle : 0.802 14.289 23935 Z= 0.421 Chirality : 0.048 0.292 2639 Planarity : 0.006 0.117 3106 Dihedral : 9.538 67.843 2583 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.82 % Favored : 91.00 % Rotamer: Outliers : 2.78 % Allowed : 15.60 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.14 % 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: -4.17 (0.15), residues: 2200 helix: -4.26 (0.92), residues: 19 sheet: -2.88 (0.17), residues: 597 loop : -2.90 (0.13), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1344 TYR 0.020 0.002 TYR A1139 PHE 0.029 0.002 PHE A1045 TRP 0.015 0.002 TRP A 161 HIS 0.004 0.001 HIS A1650 Details of bonding type rmsd covalent geometry : bond 0.00418 (17524) covalent geometry : angle 0.78745 (23796) SS BOND : bond 0.00462 ( 59) SS BOND : angle 1.50987 ( 118) hydrogen bonds : bond 0.04640 ( 329) hydrogen bonds : angle 8.69304 ( 837) Misc. bond : bond 0.00051 ( 2) link_BETA1-4 : bond 0.00568 ( 3) link_BETA1-4 : angle 2.41360 ( 9) link_NAG-ASN : bond 0.00509 ( 4) link_NAG-ASN : angle 5.16402 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 187 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 TYR cc_start: 0.8651 (m-80) cc_final: 0.8445 (m-80) REVERT: A 472 LYS cc_start: 0.7697 (tttm) cc_final: 0.7143 (pttp) REVERT: A 718 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7143 (ptt-90) REVERT: A 787 ASP cc_start: 0.7410 (t70) cc_final: 0.6965 (p0) REVERT: A 1198 GLU cc_start: 0.7188 (tp30) cc_final: 0.6818 (tp30) REVERT: A 1330 LYS cc_start: 0.6519 (tttt) cc_final: 0.6312 (tttm) REVERT: A 1423 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.6204 (mm110) REVERT: A 1592 TYR cc_start: 0.7447 (t80) cc_final: 0.7016 (t80) REVERT: A 1699 PHE cc_start: 0.8521 (m-80) cc_final: 0.7902 (m-10) REVERT: A 2241 CYS cc_start: -0.1122 (OUTLIER) cc_final: -0.2151 (t) outliers start: 53 outliers final: 24 residues processed: 227 average time/residue: 0.1179 time to fit residues: 42.7696 Evaluate side-chains 181 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 925 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1084 LEU Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1373 TYR Chi-restraints excluded: chain A residue 1423 GLN Chi-restraints excluded: chain A residue 1444 VAL Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1617 SER Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1959 THR Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 2233 VAL Chi-restraints excluded: chain A residue 2241 CYS Chi-restraints excluded: chain A residue 2249 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 125 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 192 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 507 ASN A 515 GLN ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 ASN A1020 GLN ** A1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 HIS ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1665 ASN A1774 HIS A1888 GLN A2227 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.192786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.162159 restraints weight = 22942.598| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 1.86 r_work: 0.3762 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 17592 Z= 0.150 Angle : 0.720 10.858 23935 Z= 0.377 Chirality : 0.047 0.254 2639 Planarity : 0.005 0.115 3106 Dihedral : 8.167 74.223 2580 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.18 % Favored : 90.64 % Rotamer: Outliers : 4.25 % Allowed : 16.96 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.10 % 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: -3.77 (0.15), residues: 2200 helix: -3.42 (1.47), residues: 12 sheet: -2.46 (0.18), residues: 586 loop : -2.70 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1877 TYR 0.016 0.002 TYR A1139 PHE 0.027 0.002 PHE A1307 TRP 0.014 0.001 TRP A 924 HIS 0.003 0.001 HIS A2282 Details of bonding type rmsd covalent geometry : bond 0.00356 (17524) covalent geometry : angle 0.70794 (23796) SS BOND : bond 0.00415 ( 59) SS BOND : angle 1.49458 ( 118) hydrogen bonds : bond 0.03708 ( 329) hydrogen bonds : angle 7.90304 ( 837) Misc. bond : bond 0.00069 ( 2) link_BETA1-4 : bond 0.00392 ( 3) link_BETA1-4 : angle 2.32897 ( 9) link_NAG-ASN : bond 0.00444 ( 4) link_NAG-ASN : angle 3.64561 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 192 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ASP cc_start: 0.7512 (t70) cc_final: 0.7239 (t70) REVERT: A 1191 PHE cc_start: 0.4642 (OUTLIER) cc_final: 0.3196 (m-80) REVERT: A 1248 ASN cc_start: 0.7380 (t0) cc_final: 0.6736 (m110) REVERT: A 1330 LYS cc_start: 0.6478 (tttt) cc_final: 0.6268 (tttm) REVERT: A 1423 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6117 (mm-40) REVERT: A 1665 ASN cc_start: 0.5295 (OUTLIER) cc_final: 0.5004 (p0) REVERT: A 1690 ASP cc_start: 0.5135 (m-30) cc_final: 0.4927 (m-30) REVERT: A 1699 PHE cc_start: 0.8400 (m-80) cc_final: 0.8161 (m-80) REVERT: A 2241 CYS cc_start: -0.1048 (OUTLIER) cc_final: -0.2287 (t) outliers start: 81 outliers final: 41 residues processed: 259 average time/residue: 0.1114 time to fit residues: 46.5761 Evaluate side-chains 210 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 165 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 TRP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 680 CYS Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1373 TYR Chi-restraints excluded: chain A residue 1399 ASN Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1423 GLN Chi-restraints excluded: chain A residue 1444 VAL Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1665 ASN Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1670 ILE Chi-restraints excluded: chain A residue 1671 ASP Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1797 GLU Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1959 THR Chi-restraints excluded: chain A residue 1972 VAL Chi-restraints excluded: chain A residue 2038 CYS Chi-restraints excluded: chain A residue 2241 CYS Chi-restraints excluded: chain A residue 2287 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 155 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 204 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 chunk 206 optimal weight: 20.0000 chunk 93 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN A 976 ASN ** A1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1665 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.186059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.149812 restraints weight = 22962.463| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.25 r_work: 0.3600 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 17592 Z= 0.247 Angle : 0.786 12.124 23935 Z= 0.410 Chirality : 0.049 0.242 2639 Planarity : 0.005 0.109 3106 Dihedral : 7.889 70.767 2576 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.45 % Favored : 88.36 % Rotamer: Outliers : 5.04 % Allowed : 18.12 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.10 % 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: -3.69 (0.16), residues: 2200 helix: -3.47 (1.42), residues: 12 sheet: -2.31 (0.19), residues: 617 loop : -2.68 (0.14), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1877 TYR 0.021 0.002 TYR A 723 PHE 0.032 0.002 PHE A1078 TRP 0.016 0.002 TRP A 924 HIS 0.004 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00586 (17524) covalent geometry : angle 0.77411 (23796) SS BOND : bond 0.00554 ( 59) SS BOND : angle 1.70298 ( 118) hydrogen bonds : bond 0.03724 ( 329) hydrogen bonds : angle 7.78679 ( 837) Misc. bond : bond 0.00023 ( 2) link_BETA1-4 : bond 0.00454 ( 3) link_BETA1-4 : angle 2.17766 ( 9) link_NAG-ASN : bond 0.00180 ( 4) link_NAG-ASN : angle 3.62639 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 178 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ILE cc_start: 0.8738 (pt) cc_final: 0.8537 (pt) REVERT: A 265 ARG cc_start: 0.7938 (mtm-85) cc_final: 0.7313 (mtm-85) REVERT: A 599 ASP cc_start: 0.7644 (t70) cc_final: 0.7102 (t0) REVERT: A 617 GLU cc_start: 0.8132 (tt0) cc_final: 0.7926 (tt0) REVERT: A 976 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7629 (t0) REVERT: A 1191 PHE cc_start: 0.4919 (OUTLIER) cc_final: 0.3906 (m-80) REVERT: A 1248 ASN cc_start: 0.7693 (t0) cc_final: 0.6994 (m110) REVERT: A 1252 LEU cc_start: 0.8729 (mt) cc_final: 0.8493 (mt) REVERT: A 1330 LYS cc_start: 0.6910 (tttt) cc_final: 0.6699 (tttm) REVERT: A 1423 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.5951 (mm-40) REVERT: A 2241 CYS cc_start: -0.1487 (OUTLIER) cc_final: -0.2847 (t) outliers start: 96 outliers final: 61 residues processed: 257 average time/residue: 0.1126 time to fit residues: 45.8831 Evaluate side-chains 224 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 159 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 161 TRP Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 976 ASN Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1201 HIS Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1373 TYR Chi-restraints excluded: chain A residue 1399 ASN Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1423 GLN Chi-restraints excluded: chain A residue 1426 SER Chi-restraints excluded: chain A residue 1444 VAL Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1656 GLU Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1671 ASP Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1797 GLU Chi-restraints excluded: chain A residue 1802 LEU Chi-restraints excluded: chain A residue 1881 MET Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1927 VAL Chi-restraints excluded: chain A residue 1959 THR Chi-restraints excluded: chain A residue 1972 VAL Chi-restraints excluded: chain A residue 2038 CYS Chi-restraints excluded: chain A residue 2109 VAL Chi-restraints excluded: chain A residue 2115 THR Chi-restraints excluded: chain A residue 2233 VAL Chi-restraints excluded: chain A residue 2241 CYS Chi-restraints excluded: chain A residue 2287 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 29 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 175 optimal weight: 0.0050 chunk 179 optimal weight: 0.9990 chunk 143 optimal weight: 0.0980 chunk 178 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1520 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.192951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.159279 restraints weight = 22636.236| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.00 r_work: 0.3734 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 17592 Z= 0.128 Angle : 0.683 10.414 23935 Z= 0.358 Chirality : 0.046 0.268 2639 Planarity : 0.005 0.104 3106 Dihedral : 7.169 68.706 2575 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.86 % Favored : 90.95 % Rotamer: Outliers : 4.20 % Allowed : 19.54 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.10 % 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: -3.51 (0.16), residues: 2200 helix: -3.37 (1.46), residues: 12 sheet: -2.15 (0.19), residues: 631 loop : -2.56 (0.14), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1877 TYR 0.014 0.001 TYR A 72 PHE 0.024 0.002 PHE A1978 TRP 0.013 0.001 TRP A 916 HIS 0.003 0.001 HIS A 284 Details of bonding type rmsd covalent geometry : bond 0.00298 (17524) covalent geometry : angle 0.67224 (23796) SS BOND : bond 0.00336 ( 59) SS BOND : angle 1.45106 ( 118) hydrogen bonds : bond 0.03222 ( 329) hydrogen bonds : angle 7.35040 ( 837) Misc. bond : bond 0.00026 ( 2) link_BETA1-4 : bond 0.00391 ( 3) link_BETA1-4 : angle 2.01239 ( 9) link_NAG-ASN : bond 0.00489 ( 4) link_NAG-ASN : angle 3.12358 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 199 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 GLU cc_start: 0.6767 (tp30) cc_final: 0.6502 (mm-30) REVERT: A 599 ASP cc_start: 0.7459 (t70) cc_final: 0.7181 (t70) REVERT: A 813 THR cc_start: 0.7118 (OUTLIER) cc_final: 0.6896 (m) REVERT: A 1191 PHE cc_start: 0.4754 (OUTLIER) cc_final: 0.3941 (m-80) REVERT: A 1216 TYR cc_start: 0.5553 (m-80) cc_final: 0.5255 (m-80) REVERT: A 1330 LYS cc_start: 0.6637 (tttt) cc_final: 0.6397 (tttm) REVERT: A 1401 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7345 (tm-30) REVERT: A 1423 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.5938 (mm-40) REVERT: A 1459 LEU cc_start: 0.8245 (mp) cc_final: 0.8036 (mt) REVERT: A 1592 TYR cc_start: 0.7614 (t80) cc_final: 0.7316 (t80) REVERT: A 1747 ASN cc_start: 0.4965 (p0) cc_final: 0.4306 (t0) REVERT: A 1989 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6825 (mm-30) outliers start: 80 outliers final: 45 residues processed: 264 average time/residue: 0.1201 time to fit residues: 50.4000 Evaluate side-chains 218 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 161 TRP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 637 THR Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 911 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1207 THR Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1399 ASN Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1423 GLN Chi-restraints excluded: chain A residue 1444 VAL Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1671 ASP Chi-restraints excluded: chain A residue 1677 HIS Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1797 GLU Chi-restraints excluded: chain A residue 1849 THR Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1939 THR Chi-restraints excluded: chain A residue 1972 VAL Chi-restraints excluded: chain A residue 2038 CYS Chi-restraints excluded: chain A residue 2233 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 126 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 3 optimal weight: 0.0050 chunk 205 optimal weight: 10.0000 chunk 144 optimal weight: 0.0980 chunk 98 optimal weight: 0.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1160 ASN ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1534 HIS A1888 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.194731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.162961 restraints weight = 22747.346| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.88 r_work: 0.3760 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 17592 Z= 0.126 Angle : 0.679 10.260 23935 Z= 0.354 Chirality : 0.046 0.219 2639 Planarity : 0.005 0.101 3106 Dihedral : 6.861 65.467 2574 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.82 % Favored : 90.05 % Rotamer: Outliers : 4.78 % Allowed : 20.22 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.05 % 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: -3.33 (0.16), residues: 2200 helix: -3.46 (1.39), residues: 12 sheet: -1.97 (0.19), residues: 643 loop : -2.46 (0.14), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1877 TYR 0.014 0.001 TYR A1551 PHE 0.022 0.002 PHE A1045 TRP 0.013 0.001 TRP A 318 HIS 0.003 0.001 HIS A1144 Details of bonding type rmsd covalent geometry : bond 0.00300 (17524) covalent geometry : angle 0.66863 (23796) SS BOND : bond 0.00326 ( 59) SS BOND : angle 1.46090 ( 118) hydrogen bonds : bond 0.03116 ( 329) hydrogen bonds : angle 7.06917 ( 837) Misc. bond : bond 0.00019 ( 2) link_BETA1-4 : bond 0.00293 ( 3) link_BETA1-4 : angle 1.70123 ( 9) link_NAG-ASN : bond 0.00281 ( 4) link_NAG-ASN : angle 2.94389 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 190 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 LEU cc_start: 0.8851 (mm) cc_final: 0.8626 (mt) REVERT: A 504 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7310 (mt) REVERT: A 787 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7194 (p0) REVERT: A 813 THR cc_start: 0.7203 (OUTLIER) cc_final: 0.6978 (m) REVERT: A 1191 PHE cc_start: 0.4657 (OUTLIER) cc_final: 0.3864 (m-80) REVERT: A 1330 LYS cc_start: 0.6577 (tttt) cc_final: 0.6316 (tttm) REVERT: A 1401 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7396 (tm-30) REVERT: A 1423 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.5852 (mm-40) REVERT: A 1651 THR cc_start: 0.7844 (OUTLIER) cc_final: 0.7589 (m) REVERT: A 2241 CYS cc_start: -0.1036 (OUTLIER) cc_final: -0.1743 (t) outliers start: 91 outliers final: 60 residues processed: 262 average time/residue: 0.1175 time to fit residues: 49.4864 Evaluate side-chains 239 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 172 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 161 TRP Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 814 TRP Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1201 HIS Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1292 GLN Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1363 GLU Chi-restraints excluded: chain A residue 1373 TYR Chi-restraints excluded: chain A residue 1399 ASN Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1423 GLN Chi-restraints excluded: chain A residue 1444 VAL Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1576 PHE Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1651 THR Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1672 LEU Chi-restraints excluded: chain A residue 1677 HIS Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1802 LEU Chi-restraints excluded: chain A residue 1849 THR Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1939 THR Chi-restraints excluded: chain A residue 1955 THR Chi-restraints excluded: chain A residue 1959 THR Chi-restraints excluded: chain A residue 1972 VAL Chi-restraints excluded: chain A residue 2115 THR Chi-restraints excluded: chain A residue 2218 THR Chi-restraints excluded: chain A residue 2233 VAL Chi-restraints excluded: chain A residue 2241 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 6 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 175 optimal weight: 0.1980 chunk 115 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 93 optimal weight: 0.0670 chunk 191 optimal weight: 9.9990 chunk 144 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1399 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.196215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.166772 restraints weight = 22814.275| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 1.74 r_work: 0.3811 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 17592 Z= 0.123 Angle : 0.659 10.059 23935 Z= 0.343 Chirality : 0.045 0.215 2639 Planarity : 0.005 0.097 3106 Dihedral : 6.635 63.987 2574 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.32 % Favored : 90.55 % Rotamer: Outliers : 4.36 % Allowed : 21.11 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.05 % 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: -3.14 (0.17), residues: 2200 helix: -3.00 (2.50), residues: 6 sheet: -1.79 (0.19), residues: 643 loop : -2.37 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 718 TYR 0.014 0.001 TYR A1592 PHE 0.021 0.001 PHE A1307 TRP 0.013 0.001 TRP A 318 HIS 0.003 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00294 (17524) covalent geometry : angle 0.65061 (23796) SS BOND : bond 0.00345 ( 59) SS BOND : angle 1.28516 ( 118) hydrogen bonds : bond 0.02932 ( 329) hydrogen bonds : angle 6.80043 ( 837) Misc. bond : bond 0.00016 ( 2) link_BETA1-4 : bond 0.00301 ( 3) link_BETA1-4 : angle 1.48358 ( 9) link_NAG-ASN : bond 0.00327 ( 4) link_NAG-ASN : angle 2.85381 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 184 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.7160 (mtp) cc_final: 0.6810 (mtp) REVERT: A 187 LEU cc_start: 0.8835 (mm) cc_final: 0.8604 (mt) REVERT: A 472 LYS cc_start: 0.7494 (tttm) cc_final: 0.6951 (pttp) REVERT: A 504 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7174 (mt) REVERT: A 515 GLN cc_start: 0.6341 (tm-30) cc_final: 0.5431 (mp10) REVERT: A 787 ASP cc_start: 0.7391 (t70) cc_final: 0.6912 (p0) REVERT: A 813 THR cc_start: 0.7205 (OUTLIER) cc_final: 0.6960 (m) REVERT: A 1191 PHE cc_start: 0.4567 (OUTLIER) cc_final: 0.3959 (m-80) REVERT: A 1401 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7328 (tm-30) REVERT: A 1747 ASN cc_start: 0.5002 (p0) cc_final: 0.4374 (t0) REVERT: A 2241 CYS cc_start: -0.0891 (OUTLIER) cc_final: -0.1681 (t) outliers start: 83 outliers final: 62 residues processed: 252 average time/residue: 0.1160 time to fit residues: 46.7805 Evaluate side-chains 241 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 175 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 161 TRP Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 814 TRP Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1201 HIS Chi-restraints excluded: chain A residue 1207 THR Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1292 GLN Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1363 GLU Chi-restraints excluded: chain A residue 1373 TYR Chi-restraints excluded: chain A residue 1399 ASN Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1576 PHE Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1651 THR Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1672 LEU Chi-restraints excluded: chain A residue 1677 HIS Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1802 LEU Chi-restraints excluded: chain A residue 1849 THR Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1939 THR Chi-restraints excluded: chain A residue 1955 THR Chi-restraints excluded: chain A residue 1972 VAL Chi-restraints excluded: chain A residue 2115 THR Chi-restraints excluded: chain A residue 2218 THR Chi-restraints excluded: chain A residue 2233 VAL Chi-restraints excluded: chain A residue 2241 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 199 optimal weight: 10.0000 chunk 211 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 125 optimal weight: 0.6980 chunk 197 optimal weight: 20.0000 chunk 137 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.191509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.159395 restraints weight = 22926.893| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.13 r_work: 0.3682 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 17592 Z= 0.194 Angle : 0.712 10.063 23935 Z= 0.371 Chirality : 0.047 0.215 2639 Planarity : 0.005 0.095 3106 Dihedral : 6.722 62.749 2571 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.82 % Favored : 89.09 % Rotamer: Outliers : 4.31 % Allowed : 21.85 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.05 % 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: -3.13 (0.17), residues: 2200 helix: -3.11 (2.50), residues: 6 sheet: -1.84 (0.19), residues: 662 loop : -2.32 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1641 TYR 0.019 0.002 TYR A 473 PHE 0.026 0.002 PHE A1078 TRP 0.016 0.002 TRP A 318 HIS 0.006 0.001 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00465 (17524) covalent geometry : angle 0.70300 (23796) SS BOND : bond 0.00422 ( 59) SS BOND : angle 1.48335 ( 118) hydrogen bonds : bond 0.03099 ( 329) hydrogen bonds : angle 6.88393 ( 837) Misc. bond : bond 0.00013 ( 2) link_BETA1-4 : bond 0.00370 ( 3) link_BETA1-4 : angle 1.26766 ( 9) link_NAG-ASN : bond 0.00167 ( 4) link_NAG-ASN : angle 3.06298 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 173 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 LEU cc_start: 0.8934 (mm) cc_final: 0.8680 (mt) REVERT: A 504 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7420 (mt) REVERT: A 515 GLN cc_start: 0.6427 (tm-30) cc_final: 0.5634 (mp10) REVERT: A 813 THR cc_start: 0.7007 (OUTLIER) cc_final: 0.6767 (m) REVERT: A 1191 PHE cc_start: 0.4868 (OUTLIER) cc_final: 0.4299 (m-80) REVERT: A 1401 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7409 (tm-30) REVERT: A 2241 CYS cc_start: -0.0524 (OUTLIER) cc_final: -0.1264 (t) outliers start: 82 outliers final: 66 residues processed: 236 average time/residue: 0.1190 time to fit residues: 45.0756 Evaluate side-chains 236 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 166 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 161 TRP Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 814 TRP Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1201 HIS Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1292 GLN Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1363 GLU Chi-restraints excluded: chain A residue 1373 TYR Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1576 PHE Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1651 THR Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1671 ASP Chi-restraints excluded: chain A residue 1672 LEU Chi-restraints excluded: chain A residue 1677 HIS Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1797 GLU Chi-restraints excluded: chain A residue 1802 LEU Chi-restraints excluded: chain A residue 1849 THR Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1939 THR Chi-restraints excluded: chain A residue 1955 THR Chi-restraints excluded: chain A residue 1972 VAL Chi-restraints excluded: chain A residue 2115 THR Chi-restraints excluded: chain A residue 2218 THR Chi-restraints excluded: chain A residue 2233 VAL Chi-restraints excluded: chain A residue 2241 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 47 optimal weight: 0.6980 chunk 157 optimal weight: 0.0270 chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 0.0970 chunk 170 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 215 optimal weight: 30.0000 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.194549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.159080 restraints weight = 22945.265| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.30 r_work: 0.3734 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3602 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 17592 Z= 0.122 Angle : 0.666 12.451 23935 Z= 0.344 Chirality : 0.045 0.306 2639 Planarity : 0.005 0.093 3106 Dihedral : 6.441 61.483 2571 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.23 % Favored : 90.68 % Rotamer: Outliers : 4.25 % Allowed : 22.11 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % 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: -3.02 (0.17), residues: 2200 helix: -2.91 (2.58), residues: 6 sheet: -1.72 (0.19), residues: 674 loop : -2.27 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1877 TYR 0.016 0.001 TYR A1139 PHE 0.019 0.001 PHE A1045 TRP 0.018 0.001 TRP A 318 HIS 0.008 0.001 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00295 (17524) covalent geometry : angle 0.65939 (23796) SS BOND : bond 0.00298 ( 59) SS BOND : angle 1.13076 ( 118) hydrogen bonds : bond 0.02877 ( 329) hydrogen bonds : angle 6.62701 ( 837) Misc. bond : bond 0.00020 ( 2) link_BETA1-4 : bond 0.00343 ( 3) link_BETA1-4 : angle 1.23264 ( 9) link_NAG-ASN : bond 0.00355 ( 4) link_NAG-ASN : angle 2.77805 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 187 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.8214 (ttm) cc_final: 0.7963 (ttm) REVERT: A 187 LEU cc_start: 0.8870 (mm) cc_final: 0.8620 (mt) REVERT: A 265 ARG cc_start: 0.7887 (mtm-85) cc_final: 0.7481 (mtm-85) REVERT: A 504 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7240 (mt) REVERT: A 515 GLN cc_start: 0.6306 (tm-30) cc_final: 0.5525 (mp10) REVERT: A 787 ASP cc_start: 0.7439 (t70) cc_final: 0.6972 (p0) REVERT: A 813 THR cc_start: 0.7107 (OUTLIER) cc_final: 0.6885 (m) REVERT: A 954 ASP cc_start: 0.6690 (m-30) cc_final: 0.6402 (m-30) REVERT: A 1191 PHE cc_start: 0.4887 (OUTLIER) cc_final: 0.4663 (m-80) REVERT: A 1747 ASN cc_start: 0.4876 (p0) cc_final: 0.4284 (t0) REVERT: A 2241 CYS cc_start: -0.0433 (OUTLIER) cc_final: -0.1226 (t) outliers start: 81 outliers final: 60 residues processed: 251 average time/residue: 0.1205 time to fit residues: 48.3785 Evaluate side-chains 239 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 175 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 161 TRP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 576 SER Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 814 TRP Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1201 HIS Chi-restraints excluded: chain A residue 1207 THR Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1292 GLN Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1363 GLU Chi-restraints excluded: chain A residue 1373 TYR Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1576 PHE Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1651 THR Chi-restraints excluded: chain A residue 1661 CYS Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1672 LEU Chi-restraints excluded: chain A residue 1677 HIS Chi-restraints excluded: chain A residue 1701 ILE Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1797 GLU Chi-restraints excluded: chain A residue 1802 LEU Chi-restraints excluded: chain A residue 1849 THR Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1955 THR Chi-restraints excluded: chain A residue 1972 VAL Chi-restraints excluded: chain A residue 2218 THR Chi-restraints excluded: chain A residue 2233 VAL Chi-restraints excluded: chain A residue 2241 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 132 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 154 optimal weight: 0.0060 chunk 86 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 chunk 190 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS A1399 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.194259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.158618 restraints weight = 22916.301| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.15 r_work: 0.3747 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 17592 Z= 0.134 Angle : 0.662 11.634 23935 Z= 0.343 Chirality : 0.045 0.220 2639 Planarity : 0.005 0.091 3106 Dihedral : 6.389 60.674 2571 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.73 % Favored : 90.18 % Rotamer: Outliers : 3.41 % Allowed : 22.95 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.17), residues: 2200 helix: -3.24 (1.50), residues: 12 sheet: -1.65 (0.19), residues: 672 loop : -2.22 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 244 TYR 0.016 0.001 TYR A1139 PHE 0.020 0.001 PHE A1307 TRP 0.019 0.001 TRP A 318 HIS 0.011 0.001 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00324 (17524) covalent geometry : angle 0.65514 (23796) SS BOND : bond 0.00323 ( 59) SS BOND : angle 1.15893 ( 118) hydrogen bonds : bond 0.02841 ( 329) hydrogen bonds : angle 6.56211 ( 837) Misc. bond : bond 0.00010 ( 2) link_BETA1-4 : bond 0.00447 ( 3) link_BETA1-4 : angle 1.21479 ( 9) link_NAG-ASN : bond 0.00278 ( 4) link_NAG-ASN : angle 3.15500 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 176 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 LEU cc_start: 0.8858 (mm) cc_final: 0.8621 (mt) REVERT: A 265 ARG cc_start: 0.7893 (mtm-85) cc_final: 0.7489 (mtm-85) REVERT: A 504 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7203 (mt) REVERT: A 515 GLN cc_start: 0.6290 (tm-30) cc_final: 0.5517 (mp10) REVERT: A 787 ASP cc_start: 0.7444 (t70) cc_final: 0.6969 (p0) REVERT: A 813 THR cc_start: 0.7121 (OUTLIER) cc_final: 0.6893 (m) REVERT: A 954 ASP cc_start: 0.6760 (m-30) cc_final: 0.6470 (m-30) REVERT: A 1191 PHE cc_start: 0.4781 (OUTLIER) cc_final: 0.4574 (m-80) REVERT: A 1747 ASN cc_start: 0.5053 (p0) cc_final: 0.4451 (t0) REVERT: A 2241 CYS cc_start: -0.0403 (OUTLIER) cc_final: -0.1270 (t) outliers start: 65 outliers final: 58 residues processed: 229 average time/residue: 0.1234 time to fit residues: 44.7320 Evaluate side-chains 233 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 171 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TYR Chi-restraints excluded: chain A residue 77 CYS Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 161 TRP Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 813 THR Chi-restraints excluded: chain A residue 814 TRP Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 883 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1078 PHE Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1097 ASP Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1191 PHE Chi-restraints excluded: chain A residue 1201 HIS Chi-restraints excluded: chain A residue 1236 CYS Chi-restraints excluded: chain A residue 1279 CYS Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1292 GLN Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1323 THR Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1363 GLU Chi-restraints excluded: chain A residue 1373 TYR Chi-restraints excluded: chain A residue 1414 ILE Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1576 PHE Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1651 THR Chi-restraints excluded: chain A residue 1669 LEU Chi-restraints excluded: chain A residue 1672 LEU Chi-restraints excluded: chain A residue 1677 HIS Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1797 GLU Chi-restraints excluded: chain A residue 1802 LEU Chi-restraints excluded: chain A residue 1849 THR Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1955 THR Chi-restraints excluded: chain A residue 1972 VAL Chi-restraints excluded: chain A residue 2218 THR Chi-restraints excluded: chain A residue 2233 VAL Chi-restraints excluded: chain A residue 2241 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 204 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 132 optimal weight: 0.1980 chunk 148 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 50 optimal weight: 0.2980 chunk 139 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.190513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.158985 restraints weight = 22919.696| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.04 r_work: 0.3687 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 17592 Z= 0.195 Angle : 0.712 10.894 23935 Z= 0.370 Chirality : 0.047 0.209 2639 Planarity : 0.005 0.090 3106 Dihedral : 6.608 59.562 2571 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.00 % Favored : 88.91 % Rotamer: Outliers : 3.83 % Allowed : 22.53 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.05 % 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: -3.01 (0.17), residues: 2200 helix: -3.26 (2.30), residues: 6 sheet: -1.74 (0.19), residues: 657 loop : -2.24 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1788 TYR 0.021 0.002 TYR A1216 PHE 0.028 0.002 PHE A1078 TRP 0.021 0.002 TRP A 318 HIS 0.013 0.001 HIS A 909 Details of bonding type rmsd covalent geometry : bond 0.00470 (17524) covalent geometry : angle 0.70358 (23796) SS BOND : bond 0.00414 ( 59) SS BOND : angle 1.34817 ( 118) hydrogen bonds : bond 0.02988 ( 329) hydrogen bonds : angle 6.73597 ( 837) Misc. bond : bond 0.00010 ( 2) link_BETA1-4 : bond 0.00241 ( 3) link_BETA1-4 : angle 1.05501 ( 9) link_NAG-ASN : bond 0.00286 ( 4) link_NAG-ASN : angle 3.31232 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4427.62 seconds wall clock time: 76 minutes 35.80 seconds (4595.80 seconds total)