Starting phenix.real_space_refine on Sat Sep 12 17:52:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6um1_20815/09_2026/6um1_20815.cif Found real_map, /net/cci-nas-00/data/ceres_data/6um1_20815/09_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_20815/09_2026/6um1_20815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6um1_20815/09_2026/6um1_20815.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6um1_20815/09_2026/6um1_20815.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6um1_20815/09_2026/6um1_20815.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6um1_20815/09_2026/6um1_20815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6um1_20815/09_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-2.2.1-6174/lib/python3.11/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 chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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 chiralities: 3 Time building chain proxies: 3.64, per 1000 atoms: 0.21 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: 1.53 Conformation dependent library (CDL) restraints added in 828.2 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: 1.13 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: 5.72 Time building geometry restraints manager: 2.06 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 - 21.89: 9650 21.89 - 43.78: 789 43.78 - 65.67: 111 65.67 - 87.56: 13 87.56 - 109.45: 4 Dihedral angle restraints: 10567 sinusoidal: 4195 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 10564 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: 1.990 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 19.700 Find NCS groups from input model: 0.180 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: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 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 : 15.071 109.449 6314 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/Z covalent geometry : bond 0.01398 / 1.06 (17524) covalent geometry : angle 1.82881 / 1.26 (23796) SS BOND : bond 0.00876 / 0.52 ( 59) SS BOND : angle 1.94542 / 1.24 ( 118) hydrogen bonds : bond 0.28728 / 18.67 ( 329) hydrogen bonds : angle 12.44573 / 8.57 ( 837) Misc. bond : bond 0.08958 / 4.71 ( 2) link_BETA1-4 : bond 0.00557 / 0.26 ( 3) link_BETA1-4 : angle 3.08215 / 1.97 ( 9) link_NAG-ASN : bond 0.05879 / 3.09 ( 4) link_NAG-ASN : angle 9.09856 / 4.71 ( 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 : 0.553 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: 0.1426 time to fit residues: 62.9899 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 : 0.663 ------------------------------------------------------------------------------- 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... 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 = 0.190925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.155313 restraints weight = 22933.843| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.45 r_work: 0.3650 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 17592 Z= 0.178 Angle : 0.790 13.085 23935 Z= 0.416 Chirality : 0.048 0.285 2639 Planarity : 0.006 0.116 3106 Dihedral : 8.157 61.318 2417 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.00 % Favored : 90.82 % Rotamer: Outliers : 2.94 % Allowed : 15.60 % Favored : 81.46 % 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: -4.15 (0.15), residues: 2200 helix: -4.24 (0.93), residues: 19 sheet: -2.87 (0.17), residues: 597 loop : -2.89 (0.13), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1344 TYR 0.019 0.002 TYR A1139 PHE 0.029 0.002 PHE A1045 TRP 0.014 0.002 TRP A 916 HIS 0.005 0.001 HIS A1650 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (17524) covalent geometry : angle 0.77717 / 0.41 (23796) SS BOND : bond 0.00462 / 0.27 ( 59) SS BOND : angle 1.51402 / 0.98 ( 118) hydrogen bonds : bond 0.04472 / 2.94 ( 329) hydrogen bonds : angle 8.61966 / 5.97 ( 837) Misc. bond : bond 0.00039 / 0.02 ( 2) link_BETA1-4 : bond 0.00473 / 0.20 ( 3) link_BETA1-4 : angle 1.84591 / 1.09 ( 9) link_NAG-ASN : bond 0.00491 / 0.23 ( 4) link_NAG-ASN : angle 4.80088 / 2.58 ( 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 248 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 192 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 LYS cc_start: 0.7697 (tttm) cc_final: 0.7170 (pttp) REVERT: A 718 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.7068 (ptt-90) REVERT: A 787 ASP cc_start: 0.7435 (t70) cc_final: 0.6989 (p0) REVERT: A 1198 GLU cc_start: 0.7249 (tp30) cc_final: 0.6886 (tp30) REVERT: A 1423 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.6255 (mm110) REVERT: A 1592 TYR cc_start: 0.7452 (t80) cc_final: 0.7084 (t80) REVERT: A 2241 CYS cc_start: -0.1105 (OUTLIER) cc_final: -0.2200 (t) outliers start: 56 outliers final: 23 residues processed: 235 average time/residue: 0.1261 time to fit residues: 47.1438 Evaluate side-chains 181 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 878 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 1961 VAL Chi-restraints excluded: chain A residue 2233 VAL Chi-restraints excluded: chain A residue 2241 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 125 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 154 optimal weight: 0.0170 chunk 114 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4327 r_free = 0.4327 target = 0.192260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.161138 restraints weight = 22921.407| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.96 r_work: 0.3728 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 17592 Z= 0.162 Angle : 0.723 10.893 23935 Z= 0.381 Chirality : 0.047 0.247 2639 Planarity : 0.005 0.115 3106 Dihedral : 7.464 73.758 2414 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.23 % Favored : 90.59 % Rotamer: Outliers : 4.46 % Allowed : 16.75 % Favored : 78.78 % 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: -3.77 (0.15), residues: 2200 helix: -3.40 (1.48), residues: 12 sheet: -2.44 (0.19), residues: 585 loop : -2.71 (0.14), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1877 TYR 0.018 0.002 TYR A 158 PHE 0.026 0.002 PHE A1307 TRP 0.014 0.002 TRP A 924 HIS 0.003 0.001 HIS A2282 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (17524) covalent geometry : angle 0.71321 / 0.38 (23796) SS BOND : bond 0.00383 / 0.22 ( 59) SS BOND : angle 1.42863 / 0.93 ( 118) hydrogen bonds : bond 0.03769 / 2.50 ( 329) hydrogen bonds : angle 7.87493 / 5.44 ( 837) Misc. bond : bond 0.00020 / 0.01 ( 2) link_BETA1-4 : bond 0.00450 / 0.21 ( 3) link_BETA1-4 : angle 1.63948 / 0.97 ( 9) link_NAG-ASN : bond 0.00442 / 0.23 ( 4) link_NAG-ASN : angle 3.38734 / 1.88 ( 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: 85 poor density : 188 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7899 (mtm-85) cc_final: 0.7619 (mtm-85) REVERT: A 599 ASP cc_start: 0.7577 (t70) cc_final: 0.7296 (t70) REVERT: A 1191 PHE cc_start: 0.4738 (OUTLIER) cc_final: 0.3377 (m-80) REVERT: A 1248 ASN cc_start: 0.7447 (t0) cc_final: 0.6779 (m110) REVERT: A 1423 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.6045 (mm-40) REVERT: A 1665 ASN cc_start: 0.5274 (OUTLIER) cc_final: 0.4947 (p0) REVERT: A 2241 CYS cc_start: -0.1045 (OUTLIER) cc_final: -0.2260 (t) outliers start: 85 outliers final: 46 residues processed: 258 average time/residue: 0.1194 time to fit residues: 49.7716 Evaluate side-chains 220 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 170 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 557 LEU Chi-restraints excluded: chain A residue 576 SER 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 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 1426 SER Chi-restraints excluded: chain A residue 1444 VAL Chi-restraints excluded: chain A residue 1449 VAL Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1617 SER 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 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 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: 7.9990 chunk 159 optimal weight: 8.9990 chunk 204 optimal weight: 5.9990 chunk 105 optimal weight: 0.2980 chunk 66 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 206 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** A1534 HIS A1665 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.188905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.151183 restraints weight = 22744.572| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.33 r_work: 0.3599 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 17592 Z= 0.173 Angle : 0.722 10.965 23935 Z= 0.377 Chirality : 0.046 0.220 2639 Planarity : 0.005 0.108 3106 Dihedral : 7.181 70.563 2410 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.86 % Favored : 89.95 % Rotamer: Outliers : 4.73 % Allowed : 18.01 % Favored : 77.26 % 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: -3.63 (0.16), residues: 2200 helix: -3.50 (1.38), residues: 12 sheet: -2.27 (0.19), residues: 601 loop : -2.64 (0.14), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1877 TYR 0.016 0.002 TYR A 723 PHE 0.025 0.002 PHE A1307 TRP 0.012 0.001 TRP A 161 HIS 0.004 0.001 HIS A2282 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (17524) covalent geometry : angle 0.71200 / 0.37 (23796) SS BOND : bond 0.00492 / 0.27 ( 59) SS BOND : angle 1.48613 / 0.95 ( 118) hydrogen bonds : bond 0.03465 / 2.31 ( 329) hydrogen bonds : angle 7.61068 / 5.27 ( 837) Misc. bond : bond 0.00013 / 0.01 ( 2) link_BETA1-4 : bond 0.00424 / 0.14 ( 3) link_BETA1-4 : angle 1.62981 / 0.95 ( 9) link_NAG-ASN : bond 0.00178 / 0.09 ( 4) link_NAG-ASN : angle 3.27403 / 1.82 ( 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 275 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 185 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ASP cc_start: 0.7660 (t70) cc_final: 0.7357 (t70) REVERT: A 813 THR cc_start: 0.6866 (OUTLIER) cc_final: 0.6663 (m) REVERT: A 976 ASN cc_start: 0.7860 (OUTLIER) cc_final: 0.7557 (t0) REVERT: A 1191 PHE cc_start: 0.4623 (OUTLIER) cc_final: 0.3422 (m-80) REVERT: A 1248 ASN cc_start: 0.7622 (t0) cc_final: 0.7063 (m110) REVERT: A 1423 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.5798 (mm-40) REVERT: A 1592 TYR cc_start: 0.7700 (t80) cc_final: 0.7457 (t80) REVERT: A 2241 CYS cc_start: -0.1452 (OUTLIER) cc_final: -0.2881 (t) outliers start: 90 outliers final: 58 residues processed: 258 average time/residue: 0.1230 time to fit residues: 50.5820 Evaluate side-chains 233 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 170 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 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 267 VAL 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 504 LEU Chi-restraints excluded: chain A residue 516 ARG 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 680 CYS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 784 ASP Chi-restraints excluded: chain A residue 813 THR 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 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 1449 VAL 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 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 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 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: 2.9990 chunk 67 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 179 optimal weight: 9.9990 chunk 143 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 976 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.187813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.151178 restraints weight = 22760.769| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.29 r_work: 0.3634 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 : 0.005 0.079 17592 Z= 0.195 Angle : 0.727 10.682 23935 Z= 0.381 Chirality : 0.047 0.246 2639 Planarity : 0.005 0.104 3106 Dihedral : 7.142 69.089 2410 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.77 % Favored : 89.05 % Rotamer: Outliers : 5.15 % Allowed : 19.28 % Favored : 75.58 % 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: -3.53 (1.36), residues: 12 sheet: -2.10 (0.20), residues: 597 loop : -2.59 (0.14), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1877 TYR 0.022 0.002 TYR A 665 PHE 0.026 0.002 PHE A1078 TRP 0.014 0.002 TRP A1364 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 (17524) covalent geometry : angle 0.71788 / 0.38 (23796) SS BOND : bond 0.00441 / 0.25 ( 59) SS BOND : angle 1.44078 / 0.90 ( 118) hydrogen bonds : bond 0.03451 / 2.28 ( 329) hydrogen bonds : angle 7.48767 / 5.20 ( 837) Misc. bond : bond 0.00015 / 0.01 ( 2) link_BETA1-4 : bond 0.00335 / 0.15 ( 3) link_BETA1-4 : angle 1.61436 / 0.94 ( 9) link_NAG-ASN : bond 0.00183 / 0.09 ( 4) link_NAG-ASN : angle 3.24346 / 1.82 ( 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 287 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 189 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ASP cc_start: 0.7511 (t70) cc_final: 0.7202 (t70) REVERT: A 813 THR cc_start: 0.7004 (OUTLIER) cc_final: 0.6790 (m) REVERT: A 1053 ASP cc_start: 0.6921 (m-30) cc_final: 0.6646 (m-30) REVERT: A 1191 PHE cc_start: 0.4761 (OUTLIER) cc_final: 0.3833 (m-80) REVERT: A 1248 ASN cc_start: 0.7640 (t0) cc_final: 0.7040 (m110) REVERT: A 1423 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.5890 (mm-40) REVERT: A 1793 ASP cc_start: 0.6779 (p0) cc_final: 0.6494 (t0) REVERT: A 2241 CYS cc_start: -0.1506 (OUTLIER) cc_final: -0.2909 (t) outliers start: 98 outliers final: 69 residues processed: 265 average time/residue: 0.1237 time to fit residues: 52.0774 Evaluate side-chains 245 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 172 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 146 THR Chi-restraints excluded: chain A residue 161 TRP 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 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 656 ASP Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 680 CYS 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 775 CYS 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 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 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 1201 HIS Chi-restraints excluded: chain A residue 1223 VAL 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 1288 ILE 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 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 1593 VAL 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 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 1881 MET Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1927 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 126 optimal weight: 0.1980 chunk 89 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 ASN ** A1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1520 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.189972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.158948 restraints weight = 22942.553| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 1.96 r_work: 0.3689 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 17592 Z= 0.176 Angle : 0.710 10.579 23935 Z= 0.371 Chirality : 0.046 0.218 2639 Planarity : 0.005 0.100 3106 Dihedral : 6.980 65.947 2410 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.59 % Favored : 89.27 % Rotamer: Outliers : 5.30 % Allowed : 19.70 % 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: -3.40 (0.16), residues: 2200 helix: -3.15 (2.46), residues: 6 sheet: -2.00 (0.20), residues: 610 loop : -2.53 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1877 TYR 0.015 0.002 TYR A 723 PHE 0.024 0.002 PHE A1078 TRP 0.013 0.002 TRP A1364 HIS 0.004 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (17524) covalent geometry : angle 0.70105 / 0.37 (23796) SS BOND : bond 0.00407 / 0.22 ( 59) SS BOND : angle 1.37755 / 0.85 ( 118) hydrogen bonds : bond 0.03224 / 2.18 ( 329) hydrogen bonds : angle 7.27761 / 5.05 ( 837) Misc. bond : bond 0.00013 / 0.01 ( 2) link_BETA1-4 : bond 0.00360 / 0.17 ( 3) link_BETA1-4 : angle 1.56023 / 0.90 ( 9) link_NAG-ASN : bond 0.00329 / 0.16 ( 4) link_NAG-ASN : angle 3.11956 / 1.76 ( 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 283 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 182 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 ASP cc_start: 0.7475 (t70) cc_final: 0.7200 (t70) REVERT: A 813 THR cc_start: 0.7033 (OUTLIER) cc_final: 0.6798 (m) REVERT: A 954 ASP cc_start: 0.6754 (m-30) cc_final: 0.6537 (m-30) REVERT: A 1053 ASP cc_start: 0.6985 (m-30) cc_final: 0.6777 (m-30) REVERT: A 1191 PHE cc_start: 0.4871 (OUTLIER) cc_final: 0.4346 (m-80) REVERT: A 1248 ASN cc_start: 0.7502 (t0) cc_final: 0.6946 (m110) REVERT: A 1401 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7342 (tm-30) REVERT: A 1423 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.5936 (mm110) REVERT: A 1793 ASP cc_start: 0.6817 (p0) cc_final: 0.6601 (t0) outliers start: 101 outliers final: 75 residues processed: 263 average time/residue: 0.1234 time to fit residues: 51.6132 Evaluate side-chains 247 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 169 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 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 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 608 THR 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 680 CYS 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 775 CYS 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 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 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 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 1363 GLU Chi-restraints excluded: chain A residue 1364 TRP 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 1449 VAL Chi-restraints excluded: chain A residue 1452 SER 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 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 1881 MET Chi-restraints excluded: chain A residue 1892 VAL Chi-restraints excluded: chain A residue 1927 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 2038 CYS Chi-restraints excluded: chain A residue 2115 THR Chi-restraints excluded: chain A residue 2218 THR Chi-restraints excluded: chain A residue 2233 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 6 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 111 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 93 optimal weight: 0.3980 chunk 191 optimal weight: 7.9990 chunk 144 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 HIS A 477 HIS A 507 ASN ** A 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 ASN ** A1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.192751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.161720 restraints weight = 22851.569| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 1.86 r_work: 0.3740 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 17592 Z= 0.136 Angle : 0.681 10.848 23935 Z= 0.356 Chirality : 0.045 0.217 2639 Planarity : 0.005 0.097 3106 Dihedral : 6.730 64.535 2409 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.09 % Favored : 89.77 % Rotamer: Outliers : 4.41 % Allowed : 21.48 % Favored : 74.11 % 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: -3.28 (0.17), residues: 2200 helix: -2.95 (2.65), residues: 6 sheet: -1.95 (0.19), residues: 666 loop : -2.43 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 452 TYR 0.014 0.001 TYR A1551 PHE 0.023 0.002 PHE A1307 TRP 0.016 0.001 TRP A 318 HIS 0.003 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (17524) covalent geometry : angle 0.67383 / 0.35 (23796) SS BOND : bond 0.00395 / 0.22 ( 59) SS BOND : angle 1.25368 / 0.78 ( 118) hydrogen bonds : bond 0.03029 / 2.03 ( 329) hydrogen bonds : angle 7.00574 / 4.88 ( 837) Misc. bond : bond 0.00012 / 0.01 ( 2) link_BETA1-4 : bond 0.00276 / 0.11 ( 3) link_BETA1-4 : angle 1.43174 / 0.83 ( 9) link_NAG-ASN : bond 0.00298 / 0.15 ( 4) link_NAG-ASN : angle 2.81770 / 1.56 ( 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 269 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 185 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 LEU cc_start: 0.8893 (mm) cc_final: 0.8674 (mt) REVERT: A 472 LYS cc_start: 0.7515 (tttm) cc_final: 0.6928 (pttp) REVERT: A 504 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7261 (mt) REVERT: A 599 ASP cc_start: 0.7307 (t70) cc_final: 0.7031 (t70) REVERT: A 813 THR cc_start: 0.7167 (OUTLIER) cc_final: 0.6951 (m) REVERT: A 1053 ASP cc_start: 0.6840 (m-30) cc_final: 0.6596 (m-30) REVERT: A 1191 PHE cc_start: 0.4742 (OUTLIER) cc_final: 0.4328 (m-80) REVERT: A 1401 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7333 (tm-30) REVERT: A 1651 THR cc_start: 0.7875 (OUTLIER) cc_final: 0.7631 (m) REVERT: A 1699 PHE cc_start: 0.8304 (m-80) cc_final: 0.7951 (m-80) outliers start: 84 outliers final: 61 residues processed: 253 average time/residue: 0.1239 time to fit residues: 50.2164 Evaluate side-chains 237 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 172 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 438 VAL Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 ASN 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 729 THR Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 775 CYS 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 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 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 1363 GLU Chi-restraints excluded: chain A residue 1364 TRP Chi-restraints excluded: chain A residue 1416 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 199 optimal weight: 20.0000 chunk 211 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 125 optimal weight: 0.5980 chunk 197 optimal weight: 10.0000 chunk 137 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 214 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 230 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1423 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.188698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.156966 restraints weight = 22990.527| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.14 r_work: 0.3632 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3525 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= 0.208 Angle : 0.736 10.332 23935 Z= 0.384 Chirality : 0.047 0.215 2639 Planarity : 0.005 0.095 3106 Dihedral : 6.751 63.058 2406 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.41 % Favored : 88.50 % Rotamer: Outliers : 4.94 % Allowed : 21.90 % Favored : 73.16 % 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: -3.32 (0.17), residues: 2200 helix: -3.35 (2.26), residues: 6 sheet: -1.96 (0.19), residues: 660 loop : -2.46 (0.15), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 452 TYR 0.017 0.002 TYR A 723 PHE 0.031 0.002 PHE A1078 TRP 0.017 0.002 TRP A 318 HIS 0.005 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 (17524) covalent geometry : angle 0.72655 / 0.38 (23796) SS BOND : bond 0.00531 / 0.33 ( 59) SS BOND : angle 1.46649 / 0.94 ( 118) hydrogen bonds : bond 0.03138 / 2.11 ( 329) hydrogen bonds : angle 7.10051 / 4.95 ( 837) Misc. bond : bond 0.00015 / 0.01 ( 2) link_BETA1-4 : bond 0.00407 / 0.18 ( 3) link_BETA1-4 : angle 1.56202 / 0.90 ( 9) link_NAG-ASN : bond 0.00189 / 0.09 ( 4) link_NAG-ASN : angle 3.08756 / 1.75 ( 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 268 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 174 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 LEU cc_start: 0.8971 (mm) cc_final: 0.8733 (mt) REVERT: A 504 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7429 (mt) REVERT: A 515 GLN cc_start: 0.6649 (tm-30) cc_final: 0.5581 (mp10) REVERT: A 599 ASP cc_start: 0.7484 (t70) cc_final: 0.7217 (t70) REVERT: A 813 THR cc_start: 0.6965 (OUTLIER) cc_final: 0.6735 (m) REVERT: A 954 ASP cc_start: 0.6908 (m-30) cc_final: 0.6695 (m-30) REVERT: A 964 TYR cc_start: 0.7517 (m-80) cc_final: 0.7316 (m-10) REVERT: A 1053 ASP cc_start: 0.6999 (m-30) cc_final: 0.6666 (m-30) REVERT: A 1191 PHE cc_start: 0.4986 (OUTLIER) cc_final: 0.4691 (m-80) REVERT: A 1248 ASN cc_start: 0.7673 (t0) cc_final: 0.7022 (m110) REVERT: A 1651 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7688 (m) REVERT: A 2241 CYS cc_start: -0.0635 (OUTLIER) cc_final: -0.1393 (t) outliers start: 94 outliers final: 72 residues processed: 249 average time/residue: 0.1224 time to fit residues: 48.9111 Evaluate side-chains 244 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 167 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 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 438 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 ASN 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 608 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 680 CYS 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 775 CYS 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 941 VAL 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 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 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 1364 TRP Chi-restraints excluded: chain A residue 1373 TYR Chi-restraints excluded: chain A residue 1399 ASN 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 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 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 1927 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: 0.9990 chunk 157 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 215 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 0.0050 chunk 130 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 477 HIS ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1160 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 = 0.4325 r_free = 0.4325 target = 0.192437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.156648 restraints weight = 22910.166| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.34 r_work: 0.3698 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3621 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= 0.131 Angle : 0.676 11.276 23935 Z= 0.352 Chirality : 0.045 0.213 2639 Planarity : 0.005 0.093 3106 Dihedral : 6.461 62.083 2406 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.68 % Favored : 90.23 % Rotamer: Outliers : 3.73 % Allowed : 22.90 % Favored : 73.37 % 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: -3.18 (0.17), residues: 2200 helix: -3.19 (2.36), residues: 6 sheet: -1.86 (0.19), residues: 662 loop : -2.37 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 244 TYR 0.016 0.001 TYR A1216 PHE 0.022 0.002 PHE A 360 TRP 0.018 0.002 TRP A 508 HIS 0.004 0.001 HIS A 909 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (17524) covalent geometry : angle 0.66943 / 0.35 (23796) SS BOND : bond 0.00324 / 0.17 ( 59) SS BOND : angle 1.16420 / 0.74 ( 118) hydrogen bonds : bond 0.02936 / 1.95 ( 329) hydrogen bonds : angle 6.83076 / 4.76 ( 837) Misc. bond : bond 0.00015 / 0.01 ( 2) link_BETA1-4 : bond 0.00309 / 0.12 ( 3) link_BETA1-4 : angle 1.38838 / 0.80 ( 9) link_NAG-ASN : bond 0.00317 / 0.16 ( 4) link_NAG-ASN : angle 2.74573 / 1.52 ( 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 255 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 184 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 LEU cc_start: 0.8931 (mm) cc_final: 0.8723 (mt) REVERT: A 504 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7399 (mt) REVERT: A 515 GLN cc_start: 0.6466 (tm-30) cc_final: 0.5622 (mp10) REVERT: A 813 THR cc_start: 0.7038 (OUTLIER) cc_final: 0.6799 (m) REVERT: A 964 TYR cc_start: 0.7409 (m-80) cc_final: 0.7208 (m-10) REVERT: A 1053 ASP cc_start: 0.6939 (m-30) cc_final: 0.6662 (m-30) REVERT: A 1198 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6688 (tp30) REVERT: A 1267 TYR cc_start: 0.8506 (m-80) cc_final: 0.8122 (m-80) REVERT: A 1401 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7328 (tm-30) REVERT: A 1770 LEU cc_start: 0.6712 (tt) cc_final: 0.6438 (tt) REVERT: A 2241 CYS cc_start: -0.0460 (OUTLIER) cc_final: -0.1216 (t) outliers start: 71 outliers final: 58 residues processed: 244 average time/residue: 0.1256 time to fit residues: 48.8918 Evaluate side-chains 235 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 174 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 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 212 SER 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 456 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 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 775 CYS Chi-restraints excluded: chain A residue 776 ILE 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 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 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 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 1346 THR Chi-restraints excluded: chain A residue 1363 GLU Chi-restraints excluded: chain A residue 1364 TRP 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 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 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 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: 5.9990 chunk 100 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 219 optimal weight: 8.9990 chunk 109 optimal weight: 0.7980 chunk 190 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 230 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN ** A1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.188040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.152585 restraints weight = 22853.308| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.36 r_work: 0.3619 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 17592 Z= 0.217 Angle : 0.744 11.362 23935 Z= 0.386 Chirality : 0.047 0.211 2639 Planarity : 0.005 0.091 3106 Dihedral : 6.710 61.180 2406 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.59 % Favored : 88.32 % Rotamer: Outliers : 3.89 % Allowed : 22.90 % Favored : 73.21 % 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: -3.24 (0.17), residues: 2200 helix: -3.41 (2.22), residues: 6 sheet: -1.91 (0.19), residues: 666 loop : -2.41 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 452 TYR 0.019 0.002 TYR A1216 PHE 0.032 0.002 PHE A1078 TRP 0.023 0.002 TRP A 318 HIS 0.004 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 (17524) covalent geometry : angle 0.73447 / 0.38 (23796) SS BOND : bond 0.00468 / 0.27 ( 59) SS BOND : angle 1.40303 / 0.90 ( 118) hydrogen bonds : bond 0.03024 / 2.05 ( 329) hydrogen bonds : angle 7.01636 / 4.91 ( 837) Misc. bond : bond 0.00016 / 0.01 ( 2) link_BETA1-4 : bond 0.00491 / 0.20 ( 3) link_BETA1-4 : angle 1.67785 / 0.97 ( 9) link_NAG-ASN : bond 0.00216 / 0.10 ( 4) link_NAG-ASN : angle 3.39165 / 1.96 ( 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 243 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 169 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7520 (mt) REVERT: A 515 GLN cc_start: 0.6532 (tm-30) cc_final: 0.5568 (mp10) REVERT: A 599 ASP cc_start: 0.7522 (t70) cc_final: 0.7020 (t0) REVERT: A 813 THR cc_start: 0.6891 (OUTLIER) cc_final: 0.6662 (m) REVERT: A 1053 ASP cc_start: 0.7014 (m-30) cc_final: 0.6684 (m-30) REVERT: A 1248 ASN cc_start: 0.7730 (t0) cc_final: 0.7049 (m110) REVERT: A 1267 TYR cc_start: 0.8563 (m-80) cc_final: 0.8244 (m-80) REVERT: A 1401 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7432 (tm-30) REVERT: A 1770 LEU cc_start: 0.6806 (tt) cc_final: 0.6522 (tt) REVERT: A 2241 CYS cc_start: -0.0610 (OUTLIER) cc_final: -0.1475 (t) outliers start: 74 outliers final: 60 residues processed: 233 average time/residue: 0.1246 time to fit residues: 46.2261 Evaluate side-chains 225 residues out of total 1904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 162 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 85 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 438 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 501 HIS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 507 ASN 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 669 ILE Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 735 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 775 CYS Chi-restraints excluded: chain A residue 776 ILE 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 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 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 1331 VAL Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1363 GLU Chi-restraints excluded: chain A residue 1364 TRP 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 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 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: 3.9990 chunk 70 optimal weight: 3.9990 chunk 74 optimal weight: 0.0570 chunk 132 optimal weight: 0.0170 chunk 148 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 overall best weight: 0.8938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 230 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN ** A1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.188829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.156223 restraints weight = 22897.910| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.10 r_work: 0.3657 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.220 17592 Z= 0.217 Angle : 0.894 59.200 23935 Z= 0.496 Chirality : 0.050 0.903 2639 Planarity : 0.005 0.091 3106 Dihedral : 6.708 61.124 2406 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.55 % Favored : 88.32 % Rotamer: Outliers : 4.15 % Allowed : 22.64 % Favored : 73.21 % Cbeta Deviations : 0.05 % 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: -3.24 (0.17), residues: 2200 helix: -3.41 (2.23), residues: 6 sheet: -1.91 (0.19), residues: 666 loop : -2.40 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1112 TYR 0.015 0.002 TYR A 723 PHE 0.032 0.002 PHE A1078 TRP 0.020 0.002 TRP A 318 HIS 0.003 0.001 HIS A 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 (17524) covalent geometry : angle 0.88543 / 0.49 (23796) SS BOND : bond 0.00476 / 0.27 ( 59) SS BOND : angle 1.64195 / 1.07 ( 118) hydrogen bonds : bond 0.03019 / 2.04 ( 329) hydrogen bonds : angle 7.01676 / 4.91 ( 837) Misc. bond : bond 0.00009 / 0.00 ( 2) link_BETA1-4 : bond 0.00494 / 0.20 ( 3) link_BETA1-4 : angle 1.70031 / 0.99 ( 9) link_NAG-ASN : bond 0.00210 / 0.10 ( 4) link_NAG-ASN : angle 3.37757 / 1.94 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4659.39 seconds wall clock time: 80 minutes 43.27 seconds (4843.27 seconds total)