Starting phenix.real_space_refine on Wed Mar 4 21:58:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lkz_23410/03_2026/7lkz_23410.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lkz_23410/03_2026/7lkz_23410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lkz_23410/03_2026/7lkz_23410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lkz_23410/03_2026/7lkz_23410.map" model { file = "/net/cci-nas-00/data/ceres_data/7lkz_23410/03_2026/7lkz_23410.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lkz_23410/03_2026/7lkz_23410.cif" } resolution = 3.27 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= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 296 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 2 5.21 5 S 85 5.16 5 C 10021 2.51 5 N 2551 2.21 5 O 2847 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15515 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 15117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1920, 15117 Classifications: {'peptide': 1920} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 100, 'TRANS': 1819} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 3, 'HIS:plan': 2, 'ARG:plan': 4, 'TRP:plan': 3, 'PHE:plan': 3, 'ASP:plan': 6, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 126 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 298 Unusual residues: {' MG': 2, '6OU': 3, 'ATP': 2, 'NAG': 6, 'POV': 5} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'6OU:plan-1': 3, 'POV:plan-1': 3, 'POV:plan-2': 5, 'POV:plan-3': 5} Unresolved non-hydrogen planarities: 55 Time building chain proxies: 3.25, per 1000 atoms: 0.21 Number of scatterers: 15515 At special positions: 0 Unit cell: (87.55, 94.76, 208.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 85 16.00 P 9 15.00 Mg 2 11.99 O 2847 8.00 N 2551 7.00 C 10021 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.02 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 519 " distance=2.03 Simple disulfide: pdb=" SG CYS A 641 " - pdb=" SG CYS A1490 " distance=2.03 Simple disulfide: pdb=" SG CYS A1444 " - pdb=" SG CYS A1455 " distance=2.03 Simple disulfide: pdb=" SG CYS A1488 " - pdb=" SG CYS A1502 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Links applied BETA1-3 " BMA C 3 " - " BMA C 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " BETA1-6 " BMA C 3 " - " BMA C 5 " NAG-ASN " NAG A2509 " - " ASN A 444 " " NAG A2510 " - " ASN A 504 " " NAG A2511 " - " ASN A1469 " " NAG A2512 " - " ASN A1588 " " NAG A2513 " - " ASN A1662 " " NAG A2514 " - " ASN A 98 " " NAG B 1 " - " ASN A 415 " " NAG C 1 " - " ASN A1529 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 653.9 milliseconds 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3594 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 11 sheets defined 58.3% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 3 through 21 removed outlier: 3.565A pdb=" N GLN A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 removed outlier: 3.995A pdb=" N PHE A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 37 through 46 Processing helix chain 'A' and resid 61 through 65 removed outlier: 3.543A pdb=" N GLY A 65 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 77 through 79 No H-bonds generated for 'chain 'A' and resid 77 through 79' Processing helix chain 'A' and resid 100 through 113 Processing helix chain 'A' and resid 116 through 137 Processing helix chain 'A' and resid 274 through 290 Proline residue: A 282 - end of helix removed outlier: 3.710A pdb=" N GLN A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 301 Processing helix chain 'A' and resid 310 through 323 removed outlier: 5.035A pdb=" N MET A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.819A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 345 through 350' Processing helix chain 'A' and resid 367 through 380 removed outlier: 4.195A pdb=" N ASN A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 396 removed outlier: 4.676A pdb=" N ALA A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 404 through 414 Processing helix chain 'A' and resid 415 through 444 removed outlier: 3.878A pdb=" N VAL A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 445 through 456 removed outlier: 4.321A pdb=" N ASN A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 460 Processing helix chain 'A' and resid 461 through 468 removed outlier: 3.795A pdb=" N LEU A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 519 removed outlier: 3.580A pdb=" N TYR A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N CYS A 519 " --> pdb=" O GLN A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 543 removed outlier: 3.957A pdb=" N GLU A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 607 through 623 removed outlier: 3.646A pdb=" N LEU A 611 " --> pdb=" O GLY A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 654 removed outlier: 4.041A pdb=" N ARG A 653 " --> pdb=" O ILE A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 662 removed outlier: 3.570A pdb=" N PHE A 658 " --> pdb=" O CYS A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 680 Processing helix chain 'A' and resid 683 through 688 Processing helix chain 'A' and resid 692 through 722 removed outlier: 3.950A pdb=" N ILE A 696 " --> pdb=" O SER A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 753 removed outlier: 3.703A pdb=" N THR A 753 " --> pdb=" O PHE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 762 Processing helix chain 'A' and resid 763 through 772 Processing helix chain 'A' and resid 773 through 783 removed outlier: 3.595A pdb=" N ILE A 777 " --> pdb=" O TYR A 773 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 783 " --> pdb=" O CYS A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 795 Processing helix chain 'A' and resid 797 through 814 removed outlier: 3.546A pdb=" N GLY A 803 " --> pdb=" O PRO A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 859 removed outlier: 3.868A pdb=" N GLN A 859 " --> pdb=" O TRP A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 942 removed outlier: 3.783A pdb=" N CYS A 941 " --> pdb=" O PHE A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 977 removed outlier: 3.505A pdb=" N THR A 972 " --> pdb=" O GLY A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1003 Processing helix chain 'A' and resid 1019 through 1030 Processing helix chain 'A' and resid 1034 through 1048 Processing helix chain 'A' and resid 1051 through 1055 Processing helix chain 'A' and resid 1063 through 1077 removed outlier: 3.726A pdb=" N PHE A1076 " --> pdb=" O VAL A1072 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A1077 " --> pdb=" O ALA A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1107 removed outlier: 4.038A pdb=" N SER A1099 " --> pdb=" O TYR A1095 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1126 Processing helix chain 'A' and resid 1143 through 1151 Processing helix chain 'A' and resid 1204 through 1216 removed outlier: 3.757A pdb=" N LEU A1208 " --> pdb=" O ASP A1204 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1253 Processing helix chain 'A' and resid 1268 through 1280 removed outlier: 3.958A pdb=" N ILE A1272 " --> pdb=" O PRO A1268 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1369 removed outlier: 3.996A pdb=" N ARG A1368 " --> pdb=" O GLN A1364 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A1369 " --> pdb=" O HIS A1365 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1392 removed outlier: 3.525A pdb=" N PHE A1373 " --> pdb=" O SER A1369 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU A1379 " --> pdb=" O ALA A1375 " (cutoff:3.500A) Proline residue: A1380 - end of helix Processing helix chain 'A' and resid 1406 through 1410 removed outlier: 3.727A pdb=" N TYR A1410 " --> pdb=" O PRO A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1436 Processing helix chain 'A' and resid 1467 through 1477 removed outlier: 3.535A pdb=" N THR A1471 " --> pdb=" O SER A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1547 removed outlier: 3.627A pdb=" N PHE A1533 " --> pdb=" O ASN A1529 " (cutoff:3.500A) Proline residue: A1539 - end of helix Processing helix chain 'A' and resid 1573 through 1587 Processing helix chain 'A' and resid 1592 through 1601 removed outlier: 4.499A pdb=" N GLU A1601 " --> pdb=" O GLU A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1602 through 1608 removed outlier: 3.788A pdb=" N HIS A1608 " --> pdb=" O ASP A1604 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1643 removed outlier: 3.617A pdb=" N SER A1629 " --> pdb=" O HIS A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1671 through 1693 Processing helix chain 'A' and resid 1694 through 1697 removed outlier: 3.681A pdb=" N PHE A1697 " --> pdb=" O PRO A1694 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1694 through 1697' Processing helix chain 'A' and resid 1698 through 1707 Processing helix chain 'A' and resid 1708 through 1716 Processing helix chain 'A' and resid 1719 through 1750 Processing helix chain 'A' and resid 1751 through 1756 Processing helix chain 'A' and resid 1759 through 1779 removed outlier: 3.569A pdb=" N ILE A1775 " --> pdb=" O GLY A1771 " (cutoff:3.500A) Proline residue: A1776 - end of helix Processing helix chain 'A' and resid 1780 through 1784 Processing helix chain 'A' and resid 1789 through 1817 removed outlier: 3.791A pdb=" N VAL A1793 " --> pdb=" O SER A1789 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU A1814 " --> pdb=" O THR A1810 " (cutoff:3.500A) Processing helix chain 'A' and resid 1819 through 1834 removed outlier: 3.940A pdb=" N LYS A1831 " --> pdb=" O ALA A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1836 through 1862 removed outlier: 3.626A pdb=" N GLN A1852 " --> pdb=" O LEU A1848 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A1861 " --> pdb=" O VAL A1857 " (cutoff:3.500A) Processing helix chain 'A' and resid 1875 through 1899 Processing helix chain 'A' and resid 1918 through 1931 removed outlier: 3.546A pdb=" N ALA A1922 " --> pdb=" O ASP A1918 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A1931 " --> pdb=" O ARG A1927 " (cutoff:3.500A) Processing helix chain 'A' and resid 1978 through 1987 Processing helix chain 'A' and resid 2007 through 2013 Processing helix chain 'A' and resid 2028 through 2040 removed outlier: 3.596A pdb=" N ARG A2040 " --> pdb=" O TYR A2036 " (cutoff:3.500A) Processing helix chain 'A' and resid 2043 through 2046 Processing helix chain 'A' and resid 2047 through 2057 Processing helix chain 'A' and resid 2067 through 2071 removed outlier: 3.761A pdb=" N TYR A2071 " --> pdb=" O ALA A2068 " (cutoff:3.500A) Processing helix chain 'A' and resid 2073 through 2085 removed outlier: 3.979A pdb=" N ARG A2077 " --> pdb=" O GLY A2073 " (cutoff:3.500A) Processing helix chain 'A' and resid 2102 through 2120 Processing helix chain 'A' and resid 2129 through 2136 Processing helix chain 'A' and resid 2153 through 2161 Processing helix chain 'A' and resid 2178 through 2181 Processing helix chain 'A' and resid 2182 through 2193 Processing helix chain 'A' and resid 2214 through 2225 removed outlier: 3.559A pdb=" N ILE A2218 " --> pdb=" O SER A2214 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS A2225 " --> pdb=" O LEU A2221 " (cutoff:3.500A) Processing helix chain 'A' and resid 2240 through 2252 removed outlier: 3.895A pdb=" N VAL A2244 " --> pdb=" O THR A2240 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'A' and resid 525 through 527 removed outlier: 5.985A pdb=" N ILE A 398 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LYS A 397 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL A 551 " --> pdb=" O LYS A 397 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU A 399 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 567 " --> pdb=" O GLY A1653 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A1655 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL A1656 " --> pdb=" O LEU A1405 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 946 through 949 removed outlier: 3.532A pdb=" N VAL A 946 " --> pdb=" O LYS A 936 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU A 934 " --> pdb=" O ARG A 948 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N PHE A 953 " --> pdb=" O GLY A 928 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 946 through 949 removed outlier: 3.532A pdb=" N VAL A 946 " --> pdb=" O LYS A 936 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU A 934 " --> pdb=" O ARG A 948 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU A 934 " --> pdb=" O SER A 984 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER A 984 " --> pdb=" O LEU A 934 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1005 through 1008 removed outlier: 6.529A pdb=" N GLY A1006 " --> pdb=" O ILE A1084 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ASP A1086 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N CYS A1008 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A1083 " --> pdb=" O ILE A1114 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N SER A1116 " --> pdb=" O VAL A1083 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU A1085 " --> pdb=" O SER A1116 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA A 960 " --> pdb=" O ALA A1131 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE A1133 " --> pdb=" O ALA A 960 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU A 962 " --> pdb=" O ILE A1133 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE A1130 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER A1141 " --> pdb=" O ILE A1130 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE A1132 " --> pdb=" O TYR A1139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1220 through 1223 removed outlier: 6.636A pdb=" N ILE A1230 " --> pdb=" O VAL A1222 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A1157 " --> pdb=" O PHE A1231 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A1264 " --> pdb=" O VAL A2236 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A2236 " --> pdb=" O ILE A1264 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N TYR A2234 " --> pdb=" O ASP A1266 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS A2170 " --> pdb=" O GLU A2232 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TYR A2234 " --> pdb=" O THR A2168 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR A2168 " --> pdb=" O TYR A2234 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL A2236 " --> pdb=" O ILE A2166 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE A2166 " --> pdb=" O VAL A2236 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A2197 " --> pdb=" O GLN A2209 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1413 through 1416 Processing sheet with id=AA8, first strand: chain 'A' and resid 1961 through 1962 removed outlier: 3.696A pdb=" N LEU A1938 " --> pdb=" O VAL A1962 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1943 through 1945 removed outlier: 5.750A pdb=" N LEU A1943 " --> pdb=" O ARG A1957 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A1955 " --> pdb=" O LYS A1945 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2015 through 2017 removed outlier: 6.405A pdb=" N GLY A2015 " --> pdb=" O LEU A2093 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ASP A2095 " --> pdb=" O GLY A2015 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N CYS A2017 " --> pdb=" O ASP A2095 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A2092 " --> pdb=" O VAL A2124 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N THR A2126 " --> pdb=" O VAL A2092 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU A2094 " --> pdb=" O THR A2126 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE A1968 " --> pdb=" O LEU A2125 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG A2139 " --> pdb=" O CYS A1967 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2143 through 2144 768 hydrogen bonds defined for protein. 2256 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2450 1.31 - 1.45: 4343 1.45 - 1.58: 8935 1.58 - 1.71: 16 1.71 - 1.84: 136 Bond restraints: 15880 Sorted by residual: bond pdb=" C29 POV A2506 " pdb="C210 POV A2506 " ideal model delta sigma weight residual 1.333 1.524 -0.191 2.00e-02 2.50e+03 9.08e+01 bond pdb=" C4 ATP A2518 " pdb=" C5 ATP A2518 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.06e+01 bond pdb=" C4 ATP A2517 " pdb=" C5 ATP A2517 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.98e+01 bond pdb=" C5 ATP A2518 " pdb=" C6 ATP A2518 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.80e+01 bond pdb=" C5 ATP A2517 " pdb=" C6 ATP A2517 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.76e+01 ... (remaining 15875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.72: 21415 4.72 - 9.45: 122 9.45 - 14.17: 5 14.17 - 18.90: 7 18.90 - 23.62: 2 Bond angle restraints: 21551 Sorted by residual: angle pdb=" PB ATP A2518 " pdb=" O3B ATP A2518 " pdb=" PG ATP A2518 " ideal model delta sigma weight residual 139.87 116.25 23.62 1.00e+00 1.00e+00 5.58e+02 angle pdb=" PB ATP A2517 " pdb=" O3B ATP A2517 " pdb=" PG ATP A2517 " ideal model delta sigma weight residual 139.87 119.37 20.50 1.00e+00 1.00e+00 4.20e+02 angle pdb=" PA ATP A2517 " pdb=" O3A ATP A2517 " pdb=" PB ATP A2517 " ideal model delta sigma weight residual 136.83 118.61 18.22 1.00e+00 1.00e+00 3.32e+02 angle pdb=" PA ATP A2518 " pdb=" O3A ATP A2518 " pdb=" PB ATP A2518 " ideal model delta sigma weight residual 136.83 119.31 17.52 1.00e+00 1.00e+00 3.07e+02 angle pdb=" C5 ATP A2517 " pdb=" C4 ATP A2517 " pdb=" N3 ATP A2517 " ideal model delta sigma weight residual 126.80 118.70 8.10 1.00e+00 1.00e+00 6.56e+01 ... (remaining 21546 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.29: 9161 31.29 - 62.58: 422 62.58 - 93.87: 78 93.87 - 125.17: 21 125.17 - 156.46: 3 Dihedral angle restraints: 9685 sinusoidal: 4122 harmonic: 5563 Sorted by residual: dihedral pdb=" CB CYS A 641 " pdb=" SG CYS A 641 " pdb=" SG CYS A1490 " pdb=" CB CYS A1490 " ideal model delta sinusoidal sigma weight residual 93.00 169.92 -76.92 1 1.00e+01 1.00e-02 7.43e+01 dihedral pdb=" CB CYS A1444 " pdb=" SG CYS A1444 " pdb=" SG CYS A1455 " pdb=" CB CYS A1455 " ideal model delta sinusoidal sigma weight residual 93.00 144.98 -51.98 1 1.00e+01 1.00e-02 3.69e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 81 " pdb=" CB CYS A 81 " ideal model delta sinusoidal sigma weight residual -86.00 -137.42 51.42 1 1.00e+01 1.00e-02 3.61e+01 ... (remaining 9682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.223: 2444 0.223 - 0.445: 14 0.445 - 0.668: 2 0.668 - 0.891: 0 0.891 - 1.114: 1 Chirality restraints: 2461 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 415 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.29 -1.11 2.00e-01 2.50e+01 3.10e+01 chirality pdb=" C1 NAG A2513 " pdb=" ND2 ASN A1662 " pdb=" C2 NAG A2513 " pdb=" O5 NAG A2513 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.93e+00 chirality pdb=" C1 NAG A2510 " pdb=" ND2 ASN A 504 " pdb=" C2 NAG A2510 " pdb=" O5 NAG A2510 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.89e+00 ... (remaining 2458 not shown) Planarity restraints: 2699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2509 " 0.287 2.00e-02 2.50e+03 2.46e-01 7.58e+02 pdb=" C7 NAG A2509 " -0.064 2.00e-02 2.50e+03 pdb=" C8 NAG A2509 " -0.015 2.00e-02 2.50e+03 pdb=" N2 NAG A2509 " -0.416 2.00e-02 2.50e+03 pdb=" O7 NAG A2509 " 0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2514 " 0.285 2.00e-02 2.50e+03 2.38e-01 7.09e+02 pdb=" C7 NAG A2514 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG A2514 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG A2514 " -0.402 2.00e-02 2.50e+03 pdb=" O7 NAG A2514 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1529 " 0.028 2.00e-02 2.50e+03 2.60e-02 8.47e+00 pdb=" CG ASN A1529 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A1529 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A1529 " -0.032 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " 0.030 2.00e-02 2.50e+03 ... (remaining 2696 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 94 2.49 - 3.10: 11452 3.10 - 3.70: 22451 3.70 - 4.30: 31846 4.30 - 4.90: 54709 Nonbonded interactions: 120552 Sorted by model distance: nonbonded pdb=" OE1 GLN A1477 " pdb=" NE1 TRP A1479 " model vdw 1.892 3.120 nonbonded pdb="MG MG A2516 " pdb=" O1B ATP A2517 " model vdw 1.916 2.170 nonbonded pdb=" NE2 GLN A1010 " pdb="MG MG A2516 " model vdw 1.944 2.250 nonbonded pdb="MG MG A2515 " pdb=" O1G ATP A2518 " model vdw 1.962 2.170 nonbonded pdb="MG MG A2515 " pdb=" O1B ATP A2518 " model vdw 1.963 2.170 ... (remaining 120547 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.960 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 : 0.008 0.237 15903 Z= 0.414 Angle : 1.128 33.753 21605 Z= 0.654 Chirality : 0.064 1.114 2461 Planarity : 0.008 0.246 2691 Dihedral : 19.429 156.458 6073 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 0.37 % Allowed : 1.53 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.19), residues: 1898 helix: 0.60 (0.17), residues: 1015 sheet: -2.70 (0.38), residues: 173 loop : -2.48 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1860 TYR 0.025 0.002 TYR A 400 PHE 0.039 0.002 PHE A 713 TRP 0.044 0.002 TRP A1479 HIS 0.007 0.001 HIS A1941 Details of bonding type rmsd covalent geometry : bond 0.00733 (15880) covalent geometry : angle 1.07542 (21551) SS BOND : bond 0.00645 ( 6) SS BOND : angle 4.63458 ( 12) hydrogen bonds : bond 0.16163 ( 766) hydrogen bonds : angle 6.79464 ( 2256) Misc. bond : bond 0.00067 ( 3) link_BETA1-3 : bond 0.00289 ( 1) link_BETA1-3 : angle 1.65695 ( 3) link_BETA1-4 : bond 0.00433 ( 4) link_BETA1-4 : angle 2.62664 ( 12) link_BETA1-6 : bond 0.00264 ( 1) link_BETA1-6 : angle 1.56375 ( 3) link_NAG-ASN : bond 0.08395 ( 8) link_NAG-ASN : angle 9.62393 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 174 time to evaluate : 0.553 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 388 ARG cc_start: 0.7765 (tpt170) cc_final: 0.7560 (tpp-160) REVERT: A 442 PHE cc_start: 0.6454 (m-80) cc_final: 0.5274 (t80) REVERT: A 786 MET cc_start: 0.7780 (mmm) cc_final: 0.7345 (mmt) REVERT: A 1041 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7176 (tp30) outliers start: 6 outliers final: 2 residues processed: 178 average time/residue: 0.1305 time to fit residues: 34.1901 Evaluate side-chains 146 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1955 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0170 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN A 423 HIS A 515 GLN ** A 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 ASN A 914 HIS A 956 ASN ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1555 GLN A1636 ASN ** A1799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1974 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.139464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.110834 restraints weight = 21521.401| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.97 r_work: 0.3240 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15903 Z= 0.158 Angle : 0.725 16.297 21605 Z= 0.348 Chirality : 0.048 0.598 2461 Planarity : 0.005 0.066 2691 Dihedral : 14.364 148.507 2532 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.77 % Allowed : 10.56 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.20), residues: 1898 helix: 1.00 (0.17), residues: 1011 sheet: -2.60 (0.38), residues: 171 loop : -2.31 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 511 TYR 0.017 0.001 TYR A1735 PHE 0.018 0.001 PHE A 812 TRP 0.015 0.001 TRP A 782 HIS 0.014 0.001 HIS A 914 Details of bonding type rmsd covalent geometry : bond 0.00360 (15880) covalent geometry : angle 0.69237 (21551) SS BOND : bond 0.00741 ( 6) SS BOND : angle 2.52135 ( 12) hydrogen bonds : bond 0.05019 ( 766) hydrogen bonds : angle 5.07677 ( 2256) Misc. bond : bond 0.00050 ( 3) link_BETA1-3 : bond 0.00852 ( 1) link_BETA1-3 : angle 2.07927 ( 3) link_BETA1-4 : bond 0.00777 ( 4) link_BETA1-4 : angle 3.41898 ( 12) link_BETA1-6 : bond 0.00763 ( 1) link_BETA1-6 : angle 2.98261 ( 3) link_NAG-ASN : bond 0.00591 ( 8) link_NAG-ASN : angle 5.65557 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.590 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 388 ARG cc_start: 0.8208 (tpt170) cc_final: 0.7845 (tpp-160) REVERT: A 442 PHE cc_start: 0.6413 (m-80) cc_final: 0.5191 (t80) REVERT: A 1041 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7611 (tp30) REVERT: A 1045 MET cc_start: 0.8538 (mmm) cc_final: 0.8312 (tpp) REVERT: A 1583 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8407 (mp) outliers start: 29 outliers final: 18 residues processed: 164 average time/residue: 0.1157 time to fit residues: 28.9874 Evaluate side-chains 157 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1479 TRP Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1498 MET Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1821 THR Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain A residue 2197 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 66 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 172 optimal weight: 0.5980 chunk 173 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 29 optimal weight: 0.0670 chunk 87 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 HIS A 515 GLN A 566 HIS ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1974 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.140831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112211 restraints weight = 21760.609| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.02 r_work: 0.3254 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15903 Z= 0.135 Angle : 0.651 15.778 21605 Z= 0.311 Chirality : 0.046 0.510 2461 Planarity : 0.004 0.066 2691 Dihedral : 11.937 140.004 2531 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.83 % Allowed : 13.06 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.20), residues: 1898 helix: 1.32 (0.17), residues: 1014 sheet: -2.52 (0.39), residues: 166 loop : -2.26 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 920 TYR 0.015 0.001 TYR A1735 PHE 0.012 0.001 PHE A1811 TRP 0.013 0.001 TRP A 605 HIS 0.004 0.001 HIS A1625 Details of bonding type rmsd covalent geometry : bond 0.00300 (15880) covalent geometry : angle 0.61916 (21551) SS BOND : bond 0.00485 ( 6) SS BOND : angle 1.84364 ( 12) hydrogen bonds : bond 0.04290 ( 766) hydrogen bonds : angle 4.67970 ( 2256) Misc. bond : bond 0.00046 ( 3) link_BETA1-3 : bond 0.00641 ( 1) link_BETA1-3 : angle 2.22409 ( 3) link_BETA1-4 : bond 0.00672 ( 4) link_BETA1-4 : angle 3.67862 ( 12) link_BETA1-6 : bond 0.01051 ( 1) link_BETA1-6 : angle 2.92143 ( 3) link_NAG-ASN : bond 0.00566 ( 8) link_NAG-ASN : angle 5.19043 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 388 ARG cc_start: 0.8336 (tpt170) cc_final: 0.7992 (tpp-160) REVERT: A 442 PHE cc_start: 0.6387 (m-80) cc_final: 0.5129 (t80) REVERT: A 1041 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7540 (tp30) REVERT: A 1587 MET cc_start: 0.8942 (mmm) cc_final: 0.8609 (mpp) REVERT: A 1613 ASP cc_start: 0.8169 (m-30) cc_final: 0.7859 (t0) outliers start: 30 outliers final: 21 residues processed: 162 average time/residue: 0.1221 time to fit residues: 30.0754 Evaluate side-chains 160 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 423 HIS Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1469 ASN Chi-restraints excluded: chain A residue 1479 TRP Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1857 VAL Chi-restraints excluded: chain A residue 1955 VAL Chi-restraints excluded: chain A residue 1990 THR Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2143 MET Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2205 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 165 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN ** A 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1475 GLN ** A1799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1974 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 = 0.3799 r_free = 0.3799 target = 0.140448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111484 restraints weight = 21751.458| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.01 r_work: 0.3241 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15903 Z= 0.137 Angle : 0.623 15.451 21605 Z= 0.297 Chirality : 0.045 0.491 2461 Planarity : 0.004 0.066 2691 Dihedral : 10.816 133.315 2531 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.56 % Allowed : 14.34 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.20), residues: 1898 helix: 1.48 (0.17), residues: 1013 sheet: -2.44 (0.39), residues: 168 loop : -2.21 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 920 TYR 0.014 0.001 TYR A1735 PHE 0.012 0.001 PHE A 713 TRP 0.014 0.001 TRP A 605 HIS 0.012 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00315 (15880) covalent geometry : angle 0.59193 (21551) SS BOND : bond 0.00316 ( 6) SS BOND : angle 1.32714 ( 12) hydrogen bonds : bond 0.04135 ( 766) hydrogen bonds : angle 4.52292 ( 2256) Misc. bond : bond 0.00044 ( 3) link_BETA1-3 : bond 0.00767 ( 1) link_BETA1-3 : angle 1.84071 ( 3) link_BETA1-4 : bond 0.00642 ( 4) link_BETA1-4 : angle 3.77315 ( 12) link_BETA1-6 : bond 0.01121 ( 1) link_BETA1-6 : angle 2.47397 ( 3) link_NAG-ASN : bond 0.00555 ( 8) link_NAG-ASN : angle 5.02550 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 0.492 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 388 ARG cc_start: 0.8346 (tpt170) cc_final: 0.7992 (tpp-160) REVERT: A 442 PHE cc_start: 0.6475 (m-80) cc_final: 0.5170 (t80) REVERT: A 1041 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7432 (tp30) REVERT: A 1551 TRP cc_start: 0.8507 (p90) cc_final: 0.8251 (p90) REVERT: A 1587 MET cc_start: 0.8963 (mmm) cc_final: 0.8697 (mpp) outliers start: 42 outliers final: 25 residues processed: 173 average time/residue: 0.1133 time to fit residues: 29.9640 Evaluate side-chains 161 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1469 ASN Chi-restraints excluded: chain A residue 1479 TRP Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1498 MET Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1702 ILE Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1821 THR Chi-restraints excluded: chain A residue 1857 VAL Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain A residue 1899 HIS Chi-restraints excluded: chain A residue 1955 VAL Chi-restraints excluded: chain A residue 1990 THR Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2143 MET Chi-restraints excluded: chain A residue 2168 THR Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2205 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 30 optimal weight: 50.0000 chunk 19 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 168 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 HIS A 515 GLN A 823 ASN ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1899 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.149141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115992 restraints weight = 22621.801| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.32 r_work: 0.3336 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15903 Z= 0.132 Angle : 0.599 15.259 21605 Z= 0.289 Chirality : 0.044 0.468 2461 Planarity : 0.004 0.064 2691 Dihedral : 9.993 127.196 2531 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.68 % Allowed : 15.80 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.20), residues: 1898 helix: 1.53 (0.17), residues: 1019 sheet: -2.34 (0.38), residues: 176 loop : -2.13 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 920 TYR 0.013 0.001 TYR A1735 PHE 0.020 0.001 PHE A 812 TRP 0.015 0.001 TRP A 605 HIS 0.003 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00305 (15880) covalent geometry : angle 0.57006 (21551) SS BOND : bond 0.00326 ( 6) SS BOND : angle 1.32039 ( 12) hydrogen bonds : bond 0.03974 ( 766) hydrogen bonds : angle 4.36861 ( 2256) Misc. bond : bond 0.00041 ( 3) link_BETA1-3 : bond 0.00583 ( 1) link_BETA1-3 : angle 1.92285 ( 3) link_BETA1-4 : bond 0.00679 ( 4) link_BETA1-4 : angle 3.16740 ( 12) link_BETA1-6 : bond 0.00905 ( 1) link_BETA1-6 : angle 1.85452 ( 3) link_NAG-ASN : bond 0.00570 ( 8) link_NAG-ASN : angle 4.90407 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 0.458 Fit side-chains REVERT: A 388 ARG cc_start: 0.8431 (tpt170) cc_final: 0.8051 (tpp-160) REVERT: A 442 PHE cc_start: 0.6627 (m-80) cc_final: 0.5188 (t80) REVERT: A 843 MET cc_start: 0.8222 (ttm) cc_final: 0.7968 (mtt) REVERT: A 1041 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7506 (tp30) REVERT: A 1046 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8652 (mp) REVERT: A 1551 TRP cc_start: 0.8446 (p90) cc_final: 0.8198 (p90) outliers start: 44 outliers final: 25 residues processed: 175 average time/residue: 0.1141 time to fit residues: 30.5805 Evaluate side-chains 162 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1479 TRP Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1498 MET Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1702 ILE Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1830 ARG Chi-restraints excluded: chain A residue 1857 VAL Chi-restraints excluded: chain A residue 1899 HIS Chi-restraints excluded: chain A residue 1955 VAL Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2123 VAL Chi-restraints excluded: chain A residue 2143 MET Chi-restraints excluded: chain A residue 2168 THR Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2205 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 94 optimal weight: 0.8980 chunk 136 optimal weight: 0.7980 chunk 182 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 116 optimal weight: 0.0670 chunk 127 optimal weight: 6.9990 chunk 113 optimal weight: 0.0170 chunk 158 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 overall best weight: 0.9558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 HIS A 515 GLN ** A 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1799 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 = 0.3907 r_free = 0.3907 target = 0.148282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.116075 restraints weight = 22677.762| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.44 r_work: 0.3301 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15903 Z= 0.150 Angle : 0.608 15.314 21605 Z= 0.294 Chirality : 0.045 0.468 2461 Planarity : 0.004 0.064 2691 Dihedral : 9.784 124.292 2531 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.75 % Allowed : 17.14 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.20), residues: 1898 helix: 1.51 (0.17), residues: 1024 sheet: -2.26 (0.39), residues: 174 loop : -2.13 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1647 TYR 0.013 0.001 TYR A1735 PHE 0.041 0.001 PHE A 812 TRP 0.015 0.001 TRP A 605 HIS 0.009 0.001 HIS A1899 Details of bonding type rmsd covalent geometry : bond 0.00354 (15880) covalent geometry : angle 0.58123 (21551) SS BOND : bond 0.00339 ( 6) SS BOND : angle 1.17141 ( 12) hydrogen bonds : bond 0.04067 ( 766) hydrogen bonds : angle 4.35689 ( 2256) Misc. bond : bond 0.00037 ( 3) link_BETA1-3 : bond 0.00501 ( 1) link_BETA1-3 : angle 1.97308 ( 3) link_BETA1-4 : bond 0.00607 ( 4) link_BETA1-4 : angle 3.03502 ( 12) link_BETA1-6 : bond 0.00756 ( 1) link_BETA1-6 : angle 1.61843 ( 3) link_NAG-ASN : bond 0.00536 ( 8) link_NAG-ASN : angle 4.82169 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 280 MET cc_start: 0.7158 (mmt) cc_final: 0.6837 (tpp) REVERT: A 388 ARG cc_start: 0.8372 (tpt170) cc_final: 0.8000 (tpp-160) REVERT: A 442 PHE cc_start: 0.6551 (m-80) cc_final: 0.5072 (t80) REVERT: A 1041 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7542 (tp30) REVERT: A 1046 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8664 (mp) REVERT: A 1551 TRP cc_start: 0.8462 (p90) cc_final: 0.8214 (p90) REVERT: A 1587 MET cc_start: 0.8575 (mpp) cc_final: 0.7726 (mpp) REVERT: A 1647 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6310 (mtm180) REVERT: A 1899 HIS cc_start: 0.5691 (OUTLIER) cc_final: 0.4978 (t-90) outliers start: 45 outliers final: 32 residues processed: 170 average time/residue: 0.1090 time to fit residues: 28.8789 Evaluate side-chains 172 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 423 HIS Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1469 ASN Chi-restraints excluded: chain A residue 1479 TRP Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1498 MET Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1647 ARG Chi-restraints excluded: chain A residue 1702 ILE Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1821 THR Chi-restraints excluded: chain A residue 1830 ARG Chi-restraints excluded: chain A residue 1857 VAL Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain A residue 1899 HIS Chi-restraints excluded: chain A residue 1955 VAL Chi-restraints excluded: chain A residue 1990 THR Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2123 VAL Chi-restraints excluded: chain A residue 2143 MET Chi-restraints excluded: chain A residue 2168 THR Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2205 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 HIS A 823 ASN ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1899 HIS ** A1974 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.146580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115100 restraints weight = 22654.537| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.38 r_work: 0.3272 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15903 Z= 0.184 Angle : 0.626 15.486 21605 Z= 0.304 Chirality : 0.046 0.480 2461 Planarity : 0.004 0.065 2691 Dihedral : 9.680 121.782 2531 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.99 % Allowed : 17.45 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.20), residues: 1898 helix: 1.54 (0.17), residues: 1016 sheet: -2.38 (0.38), residues: 176 loop : -2.08 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 290 TYR 0.013 0.001 TYR A 528 PHE 0.027 0.001 PHE A 812 TRP 0.015 0.001 TRP A 605 HIS 0.021 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00445 (15880) covalent geometry : angle 0.59973 (21551) SS BOND : bond 0.00440 ( 6) SS BOND : angle 1.81367 ( 12) hydrogen bonds : bond 0.04342 ( 766) hydrogen bonds : angle 4.39586 ( 2256) Misc. bond : bond 0.00049 ( 3) link_BETA1-3 : bond 0.00410 ( 1) link_BETA1-3 : angle 1.91250 ( 3) link_BETA1-4 : bond 0.00567 ( 4) link_BETA1-4 : angle 2.93159 ( 12) link_BETA1-6 : bond 0.00748 ( 1) link_BETA1-6 : angle 1.50150 ( 3) link_NAG-ASN : bond 0.00462 ( 8) link_NAG-ASN : angle 4.78892 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 0.578 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 280 MET cc_start: 0.7143 (mmt) cc_final: 0.6851 (tpp) REVERT: A 388 ARG cc_start: 0.8168 (tpt170) cc_final: 0.7900 (tpp-160) REVERT: A 442 PHE cc_start: 0.6650 (m-80) cc_final: 0.5139 (t80) REVERT: A 843 MET cc_start: 0.8178 (ttm) cc_final: 0.7870 (mtt) REVERT: A 1041 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7384 (tp30) REVERT: A 1046 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8657 (mp) REVERT: A 1587 MET cc_start: 0.8711 (mpp) cc_final: 0.7896 (mpp) outliers start: 49 outliers final: 37 residues processed: 178 average time/residue: 0.1074 time to fit residues: 30.0395 Evaluate side-chains 175 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1469 ASN Chi-restraints excluded: chain A residue 1479 TRP Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1498 MET Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1702 ILE Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1821 THR Chi-restraints excluded: chain A residue 1830 ARG Chi-restraints excluded: chain A residue 1857 VAL Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain A residue 1899 HIS Chi-restraints excluded: chain A residue 1955 VAL Chi-restraints excluded: chain A residue 1990 THR Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2123 VAL Chi-restraints excluded: chain A residue 2143 MET Chi-restraints excluded: chain A residue 2168 THR Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2205 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 119 optimal weight: 0.0050 chunk 117 optimal weight: 0.9990 chunk 107 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 180 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 HIS A 515 GLN ** A1799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1899 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.148786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.116845 restraints weight = 22604.726| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.56 r_work: 0.3333 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15903 Z= 0.122 Angle : 0.591 15.038 21605 Z= 0.284 Chirality : 0.044 0.457 2461 Planarity : 0.004 0.063 2691 Dihedral : 9.331 118.269 2531 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.75 % Allowed : 18.12 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.20), residues: 1898 helix: 1.68 (0.17), residues: 1022 sheet: -2.28 (0.39), residues: 176 loop : -2.07 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1830 TYR 0.017 0.001 TYR A 106 PHE 0.018 0.001 PHE A 812 TRP 0.016 0.001 TRP A 605 HIS 0.009 0.001 HIS A1899 Details of bonding type rmsd covalent geometry : bond 0.00275 (15880) covalent geometry : angle 0.56508 (21551) SS BOND : bond 0.00300 ( 6) SS BOND : angle 1.50827 ( 12) hydrogen bonds : bond 0.03827 ( 766) hydrogen bonds : angle 4.23858 ( 2256) Misc. bond : bond 0.00039 ( 3) link_BETA1-3 : bond 0.00490 ( 1) link_BETA1-3 : angle 1.90634 ( 3) link_BETA1-4 : bond 0.00570 ( 4) link_BETA1-4 : angle 2.82784 ( 12) link_BETA1-6 : bond 0.00790 ( 1) link_BETA1-6 : angle 1.38879 ( 3) link_NAG-ASN : bond 0.00581 ( 8) link_NAG-ASN : angle 4.69692 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 142 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 280 MET cc_start: 0.7184 (mmt) cc_final: 0.6919 (tpp) REVERT: A 388 ARG cc_start: 0.8292 (tpt170) cc_final: 0.8009 (tpp-160) REVERT: A 442 PHE cc_start: 0.6691 (OUTLIER) cc_final: 0.5132 (t80) REVERT: A 843 MET cc_start: 0.8246 (ttm) cc_final: 0.7964 (mtt) REVERT: A 1041 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7575 (tp30) REVERT: A 1587 MET cc_start: 0.8747 (mpp) cc_final: 0.7818 (mpp) outliers start: 45 outliers final: 35 residues processed: 172 average time/residue: 0.1120 time to fit residues: 29.7525 Evaluate side-chains 173 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1469 ASN Chi-restraints excluded: chain A residue 1479 TRP Chi-restraints excluded: chain A residue 1498 MET Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1702 ILE Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1821 THR Chi-restraints excluded: chain A residue 1899 HIS Chi-restraints excluded: chain A residue 1955 VAL Chi-restraints excluded: chain A residue 1990 THR Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2123 VAL Chi-restraints excluded: chain A residue 2143 MET Chi-restraints excluded: chain A residue 2168 THR Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2205 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 20 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 50.0000 chunk 150 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 HIS ** A1799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1899 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.145192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.115197 restraints weight = 22811.266| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.23 r_work: 0.3279 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15903 Z= 0.212 Angle : 0.647 15.457 21605 Z= 0.313 Chirality : 0.046 0.481 2461 Planarity : 0.005 0.066 2691 Dihedral : 9.322 116.508 2531 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.81 % Allowed : 18.49 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.20), residues: 1898 helix: 1.56 (0.17), residues: 1011 sheet: -2.37 (0.39), residues: 176 loop : -2.09 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1860 TYR 0.014 0.001 TYR A 106 PHE 0.028 0.002 PHE A1900 TRP 0.016 0.001 TRP A 605 HIS 0.010 0.001 HIS A1899 Details of bonding type rmsd covalent geometry : bond 0.00518 (15880) covalent geometry : angle 0.62260 (21551) SS BOND : bond 0.00422 ( 6) SS BOND : angle 1.64075 ( 12) hydrogen bonds : bond 0.04507 ( 766) hydrogen bonds : angle 4.38609 ( 2256) Misc. bond : bond 0.00033 ( 3) link_BETA1-3 : bond 0.00379 ( 1) link_BETA1-3 : angle 1.76070 ( 3) link_BETA1-4 : bond 0.00549 ( 4) link_BETA1-4 : angle 2.80139 ( 12) link_BETA1-6 : bond 0.00801 ( 1) link_BETA1-6 : angle 1.42351 ( 3) link_NAG-ASN : bond 0.00395 ( 8) link_NAG-ASN : angle 4.73070 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 0.558 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 280 MET cc_start: 0.7244 (mmt) cc_final: 0.6992 (tpp) REVERT: A 388 ARG cc_start: 0.8283 (tpt170) cc_final: 0.8000 (tpp-160) REVERT: A 442 PHE cc_start: 0.6780 (OUTLIER) cc_final: 0.5190 (t80) REVERT: A 599 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8353 (mp0) REVERT: A 614 MET cc_start: 0.8675 (mtm) cc_final: 0.8470 (mtp) REVERT: A 843 MET cc_start: 0.8322 (ttm) cc_final: 0.7998 (mtt) REVERT: A 943 ARG cc_start: 0.6717 (mtp-110) cc_final: 0.6509 (tmt-80) REVERT: A 1041 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7530 (tp30) REVERT: A 1587 MET cc_start: 0.8798 (mpp) cc_final: 0.7886 (mpp) outliers start: 46 outliers final: 39 residues processed: 170 average time/residue: 0.1107 time to fit residues: 29.3151 Evaluate side-chains 175 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 423 HIS Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1469 ASN Chi-restraints excluded: chain A residue 1479 TRP Chi-restraints excluded: chain A residue 1498 MET Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1702 ILE Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1821 THR Chi-restraints excluded: chain A residue 1830 ARG Chi-restraints excluded: chain A residue 1884 VAL Chi-restraints excluded: chain A residue 1899 HIS Chi-restraints excluded: chain A residue 1928 ILE Chi-restraints excluded: chain A residue 1955 VAL Chi-restraints excluded: chain A residue 1990 THR Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2123 VAL Chi-restraints excluded: chain A residue 2168 THR Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2205 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 43 optimal weight: 0.0000 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 chunk 178 optimal weight: 0.0980 chunk 5 optimal weight: 0.3980 chunk 90 optimal weight: 0.7980 overall best weight: 0.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 HIS A1240 HIS ** A1799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1899 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.149170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.116614 restraints weight = 22637.697| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.48 r_work: 0.3325 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15903 Z= 0.113 Angle : 0.593 15.141 21605 Z= 0.284 Chirality : 0.043 0.454 2461 Planarity : 0.004 0.062 2691 Dihedral : 9.048 113.389 2531 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.26 % Allowed : 19.04 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.20), residues: 1898 helix: 1.73 (0.17), residues: 1009 sheet: -2.27 (0.39), residues: 177 loop : -2.04 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1898 TYR 0.013 0.001 TYR A 106 PHE 0.026 0.001 PHE A1900 TRP 0.016 0.001 TRP A 605 HIS 0.011 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00245 (15880) covalent geometry : angle 0.56767 (21551) SS BOND : bond 0.00328 ( 6) SS BOND : angle 1.36578 ( 12) hydrogen bonds : bond 0.03804 ( 766) hydrogen bonds : angle 4.20711 ( 2256) Misc. bond : bond 0.00044 ( 3) link_BETA1-3 : bond 0.00458 ( 1) link_BETA1-3 : angle 1.79012 ( 3) link_BETA1-4 : bond 0.00550 ( 4) link_BETA1-4 : angle 2.72688 ( 12) link_BETA1-6 : bond 0.00957 ( 1) link_BETA1-6 : angle 1.31703 ( 3) link_NAG-ASN : bond 0.00645 ( 8) link_NAG-ASN : angle 4.65381 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 110 GLN cc_start: 0.8244 (mm-40) cc_final: 0.8009 (mm-40) REVERT: A 280 MET cc_start: 0.7331 (mmt) cc_final: 0.7073 (tpp) REVERT: A 388 ARG cc_start: 0.8306 (tpt170) cc_final: 0.8020 (tpp-160) REVERT: A 442 PHE cc_start: 0.6766 (OUTLIER) cc_final: 0.5185 (t80) REVERT: A 599 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8297 (mp0) REVERT: A 843 MET cc_start: 0.8241 (ttm) cc_final: 0.7954 (mtt) REVERT: A 1041 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7494 (tp30) REVERT: A 1587 MET cc_start: 0.8795 (mpp) cc_final: 0.7887 (mpp) outliers start: 37 outliers final: 30 residues processed: 163 average time/residue: 0.1144 time to fit residues: 29.4670 Evaluate side-chains 166 residues out of total 1690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1469 ASN Chi-restraints excluded: chain A residue 1479 TRP Chi-restraints excluded: chain A residue 1498 MET Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1571 ILE Chi-restraints excluded: chain A residue 1702 ILE Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1821 THR Chi-restraints excluded: chain A residue 1955 VAL Chi-restraints excluded: chain A residue 1990 THR Chi-restraints excluded: chain A residue 2123 VAL Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2205 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 30 optimal weight: 50.0000 chunk 121 optimal weight: 0.8980 chunk 83 optimal weight: 0.1980 chunk 40 optimal weight: 0.0020 chunk 117 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 HIS A1011 HIS A1353 GLN ** A1799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.149733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.117800 restraints weight = 22511.235| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.42 r_work: 0.3353 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15903 Z= 0.115 Angle : 0.579 14.684 21605 Z= 0.277 Chirality : 0.043 0.452 2461 Planarity : 0.004 0.061 2691 Dihedral : 8.695 108.717 2531 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.14 % Allowed : 19.22 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.20), residues: 1898 helix: 1.84 (0.17), residues: 1015 sheet: -2.02 (0.40), residues: 168 loop : -2.04 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1489 TYR 0.013 0.001 TYR A 106 PHE 0.020 0.001 PHE A1900 TRP 0.017 0.001 TRP A 605 HIS 0.008 0.001 HIS A1240 Details of bonding type rmsd covalent geometry : bond 0.00258 (15880) covalent geometry : angle 0.55475 (21551) SS BOND : bond 0.00316 ( 6) SS BOND : angle 1.19220 ( 12) hydrogen bonds : bond 0.03587 ( 766) hydrogen bonds : angle 4.12277 ( 2256) Misc. bond : bond 0.00037 ( 3) link_BETA1-3 : bond 0.00531 ( 1) link_BETA1-3 : angle 1.60630 ( 3) link_BETA1-4 : bond 0.00470 ( 4) link_BETA1-4 : angle 2.60419 ( 12) link_BETA1-6 : bond 0.00875 ( 1) link_BETA1-6 : angle 1.25031 ( 3) link_NAG-ASN : bond 0.00599 ( 8) link_NAG-ASN : angle 4.52668 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3650.59 seconds wall clock time: 63 minutes 14.84 seconds (3794.84 seconds total)