Starting phenix.real_space_refine on Sat Jan 20 16:51:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkz_23410/01_2024/7lkz_23410_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkz_23410/01_2024/7lkz_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkz_23410/01_2024/7lkz_23410.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkz_23410/01_2024/7lkz_23410.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkz_23410/01_2024/7lkz_23410_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lkz_23410/01_2024/7lkz_23410_updated.pdb" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "A ARG 5": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ARG 572": "NH1" <-> "NH2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A ARG 602": "NH1" <-> "NH2" Residue "A GLU 684": "OE1" <-> "OE2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A GLU 789": "OE1" <-> "OE2" Residue "A GLU 807": "OE1" <-> "OE2" Residue "A GLU 813": "OE1" <-> "OE2" Residue "A GLU 814": "OE1" <-> "OE2" Residue "A GLU 833": "OE1" <-> "OE2" Residue "A GLU 921": "OE1" <-> "OE2" Residue "A GLU 939": "OE1" <-> "OE2" Residue "A GLU 955": "OE1" <-> "OE2" Residue "A GLU 1022": "OE1" <-> "OE2" Residue "A GLU 1036": "OE1" <-> "OE2" Residue "A GLU 1037": "OE1" <-> "OE2" Residue "A GLU 1043": "OE1" <-> "OE2" Residue "A GLU 1047": "OE1" <-> "OE2" Residue "A GLU 1057": "OE1" <-> "OE2" Residue "A GLU 1058": "OE1" <-> "OE2" Residue "A ARG 1068": "NH1" <-> "NH2" Residue "A ARG 1108": "NH1" <-> "NH2" Residue "A ARG 1111": "NH1" <-> "NH2" Residue "A ARG 1129": "NH1" <-> "NH2" Residue "A ARG 1137": "NH1" <-> "NH2" Residue "A ARG 1161": "NH1" <-> "NH2" Residue "A GLU 1218": "OE1" <-> "OE2" Residue "A GLU 1223": "OE1" <-> "OE2" Residue "A GLU 1251": "OE1" <-> "OE2" Residue "A GLU 1270": "OE1" <-> "OE2" Residue "A ARG 1362": "NH1" <-> "NH2" Residue "A GLU 1504": "OE1" <-> "OE2" Residue "A ARG 1514": "NH1" <-> "NH2" Residue "A GLU 1520": "OE1" <-> "OE2" Residue "A ARG 1528": "NH1" <-> "NH2" Residue "A ARG 1543": "NH1" <-> "NH2" Residue "A ARG 1585": "NH1" <-> "NH2" Residue "A GLU 1597": "OE1" <-> "OE2" Residue "A GLU 1601": "OE1" <-> "OE2" Residue "A GLU 1612": "OE1" <-> "OE2" Residue "A ARG 1705": "NH1" <-> "NH2" Residue "A GLU 1758": "OE1" <-> "OE2" Residue "A TYR 1770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1814": "OE1" <-> "OE2" Residue "A GLU 1817": "OE1" <-> "OE2" Residue "A GLU 1863": "OE1" <-> "OE2" Residue "A GLU 1864": "OE1" <-> "OE2" Residue "A PHE 1880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1917": "OE1" <-> "OE2" Residue "A GLU 1923": "OE1" <-> "OE2" Residue "A GLU 1942": "OE1" <-> "OE2" Residue "A ARG 1963": "NH1" <-> "NH2" Residue "A GLU 1966": "OE1" <-> "OE2" Residue "A GLU 2025": "OE1" <-> "OE2" Residue "A ARG 2030": "NH1" <-> "NH2" Residue "A GLU 2031": "OE1" <-> "OE2" Residue "A ARG 2038": "NH1" <-> "NH2" Residue "A GLU 2045": "OE1" <-> "OE2" Residue "A ARG 2077": "NH1" <-> "NH2" Residue "A ARG 2107": "NH1" <-> "NH2" Residue "A ARG 2118": "NH1" <-> "NH2" Residue "A ARG 2121": "NH1" <-> "NH2" Residue "A GLU 2132": "OE1" <-> "OE2" Residue "A GLU 2134": "OE1" <-> "OE2" Residue "A ARG 2139": "NH1" <-> "NH2" Residue "A ARG 2149": "NH1" <-> "NH2" Residue "A GLU 2186": "OE1" <-> "OE2" Residue "A ARG 2201": "NH1" <-> "NH2" Residue "A GLU 2232": "OE1" <-> "OE2" Residue "A PHE 2245": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/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: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4} 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: {'POV:plan-3': 5, 'POV:plan-2': 5, 'POV:plan-1': 3, '6OU:plan-1': 3} Unresolved non-hydrogen planarities: 55 Time building chain proxies: 8.62, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 7.04 Conformation dependent library (CDL) restraints added in 2.7 seconds 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... running ksdssp... Secondary structure from input PDB file: 75 helices and 11 sheets defined 50.1% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.54 Creating SS restraints... Processing helix chain 'A' and resid 4 through 20 Processing helix chain 'A' and resid 22 through 35 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 38 through 45 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 67 through 78 removed outlier: 3.880A pdb=" N VAL A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ASN A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 117 through 136 Processing helix chain 'A' and resid 274 through 289 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 291 through 301 Processing helix chain 'A' and resid 311 through 322 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 346 through 349 No H-bonds generated for 'chain 'A' and resid 346 through 349' Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 381 through 395 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 405 through 412 Processing helix chain 'A' and resid 416 through 443 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 446 through 455 Processing helix chain 'A' and resid 457 through 460 No H-bonds generated for 'chain 'A' and resid 457 through 460' Processing helix chain 'A' and resid 462 through 467 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 531 through 544 removed outlier: 3.957A pdb=" N GLU A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 622 Processing helix chain 'A' and resid 655 through 679 removed outlier: 4.786A pdb=" N TRP A 663 " --> pdb=" O MET A 659 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 664 " --> pdb=" O VAL A 660 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N TYR A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N SER A 666 " --> pdb=" O ALA A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 687 No H-bonds generated for 'chain 'A' and resid 684 through 687' Processing helix chain 'A' and resid 693 through 721 Processing helix chain 'A' and resid 730 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 764 through 782 removed outlier: 4.190A pdb=" N TYR A 773 " --> pdb=" O TYR A 769 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 774 " --> pdb=" O PHE A 770 " (cutoff:3.500A) Proline residue: A 775 - end of helix Processing helix chain 'A' and resid 788 through 796 Processing helix chain 'A' and resid 798 through 815 removed outlier: 3.546A pdb=" N GLY A 803 " --> pdb=" O PRO A 799 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN A 815 " --> pdb=" O ARG A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 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 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 969 through 976 Processing helix chain 'A' and resid 999 through 1004 removed outlier: 4.261A pdb=" N SER A1004 " --> pdb=" O ALA A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1031 removed outlier: 4.065A pdb=" N LYS A1031 " --> pdb=" O TYR A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1047 Processing helix chain 'A' and resid 1064 through 1074 Processing helix chain 'A' and resid 1096 through 1106 removed outlier: 3.591A pdb=" N ILE A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1125 Processing helix chain 'A' and resid 1144 through 1150 Processing helix chain 'A' and resid 1205 through 1215 Processing helix chain 'A' and resid 1242 through 1252 Processing helix chain 'A' and resid 1269 through 1279 Processing helix chain 'A' and resid 1348 through 1368 removed outlier: 3.996A pdb=" N ARG A1368 " --> pdb=" O GLN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1391 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 1407 through 1409 No H-bonds generated for 'chain 'A' and resid 1407 through 1409' Processing helix chain 'A' and resid 1426 through 1435 Processing helix chain 'A' and resid 1468 through 1476 Processing helix chain 'A' and resid 1530 through 1546 Proline residue: A1539 - end of helix Processing helix chain 'A' and resid 1574 through 1587 Processing helix chain 'A' and resid 1593 through 1600 Processing helix chain 'A' and resid 1603 through 1607 Processing helix chain 'A' and resid 1626 through 1641 Processing helix chain 'A' and resid 1672 through 1692 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 1699 through 1706 Processing helix chain 'A' and resid 1709 through 1715 Processing helix chain 'A' and resid 1720 through 1749 Processing helix chain 'A' and resid 1752 through 1755 No H-bonds generated for 'chain 'A' and resid 1752 through 1755' Processing helix chain 'A' and resid 1760 through 1783 removed outlier: 3.569A pdb=" N ILE A1775 " --> pdb=" O GLY A1771 " (cutoff:3.500A) Proline residue: A1776 - end of helix Proline residue: A1780 - end of helix removed outlier: 4.573A pdb=" N PHE A1783 " --> pdb=" O TYR A1779 " (cutoff:3.500A) Processing helix chain 'A' and resid 1791 through 1816 removed outlier: 4.258A pdb=" N GLU A1814 " --> pdb=" O THR A1810 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1835 removed outlier: 3.940A pdb=" N LYS A1831 " --> pdb=" O ALA A1827 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N VAL A1835 " --> pdb=" O LYS A1831 " (cutoff:3.500A) Processing helix chain 'A' and resid 1837 through 1861 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 1876 through 1898 Processing helix chain 'A' and resid 1919 through 1930 Processing helix chain 'A' and resid 1979 through 1986 Processing helix chain 'A' and resid 2008 through 2012 Processing helix chain 'A' and resid 2029 through 2039 Processing helix chain 'A' and resid 2048 through 2056 Processing helix chain 'A' and resid 2068 through 2070 No H-bonds generated for 'chain 'A' and resid 2068 through 2070' 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 2103 through 2119 Processing helix chain 'A' and resid 2130 through 2135 Processing helix chain 'A' and resid 2154 through 2160 Processing helix chain 'A' and resid 2179 through 2192 removed outlier: 3.914A pdb=" N ASN A2183 " --> pdb=" O PRO A2180 " (cutoff:3.500A) Proline residue: A2184 - end of helix Processing helix chain 'A' and resid 2215 through 2224 Processing helix chain 'A' and resid 2241 through 2251 Processing sheet with id= A, 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: 8.023A pdb=" N LEU A 399 " --> pdb=" O TRP A 548 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY A 550 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A1653 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N TYR A 569 " --> pdb=" O GLY A1653 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR A1655 " --> pdb=" O TYR A 569 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE A 571 " --> pdb=" O THR A1655 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A1657 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 632 through 636 removed outlier: 6.306A pdb=" N ILE A1615 " --> pdb=" O TYR A 633 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLN A 635 " --> pdb=" O ILE A1615 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL A1617 " --> pdb=" O GLN A 635 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 986 through 989 removed outlier: 6.801A pdb=" N PHE A 953 " --> pdb=" O GLY A 928 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 959 through 963 removed outlier: 6.491A pdb=" N ARG A1129 " --> pdb=" O ALA A 960 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU A 962 " --> pdb=" O ARG A1129 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA A1131 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ALA A1134 " --> pdb=" O LEU A1138 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU A1138 " --> pdb=" O ALA A1134 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1005 through 1008 removed outlier: 6.614A pdb=" N VAL A1082 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N CYS A1008 " --> pdb=" O VAL A1082 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ILE A1084 " --> pdb=" O CYS A1008 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE A1114 " --> pdb=" O LEU A1085 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 1262 through 1266 removed outlier: 3.759A pdb=" N GLY A1263 " --> pdb=" O THR A1158 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A1157 " --> pdb=" O PHE A1231 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU A1232 " --> pdb=" O LEU A1221 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LEU A1221 " --> pdb=" O LEU A1232 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1413 through 1416 Processing sheet with id= H, first strand: chain 'A' and resid 1938 through 1940 Processing sheet with id= I, first strand: chain 'A' and resid 1967 through 1969 removed outlier: 6.466A pdb=" N VAL A2123 " --> pdb=" O PHE A1968 " (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: 6.405A 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) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 2196 through 2198 removed outlier: 3.997A pdb=" N VAL A2197 " --> pdb=" O GLN A2209 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1943 through 1945 removed outlier: 7.298A pdb=" N LYS A1945 " --> pdb=" O ASP A1956 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASP A1956 " --> pdb=" O LYS A1945 " (cutoff:3.500A) 643 hydrogen bonds defined for protein. 1893 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: 6.24 Time building geometry restraints manager: 7.47 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: 96.26 - 104.26: 292 104.26 - 112.25: 8138 112.25 - 120.25: 6931 120.25 - 128.25: 6032 128.25 - 136.25: 158 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: 95 2.49 - 3.10: 11530 3.10 - 3.70: 22554 3.70 - 4.30: 32100 4.30 - 4.90: 54765 Nonbonded interactions: 121044 Sorted by model distance: nonbonded pdb=" OE1 GLN A1477 " pdb=" NE1 TRP A1479 " model vdw 1.892 2.520 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 121039 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 9.920 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 45.300 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.870 ------------------------------------------------------------------------------- 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 : 0.007 0.191 15880 Z= 0.473 Angle : 1.075 23.621 21551 Z= 0.643 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 : 12.38 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.044 0.002 TRP A1479 HIS 0.007 0.001 HIS A1941 PHE 0.039 0.002 PHE A 713 TYR 0.025 0.002 TYR A 400 ARG 0.011 0.001 ARG A1860 *********************** 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 fitting. rotamer outliers: 6 poor density : 174 time to evaluate : 1.846 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: 0.3075 time to fit residues: 80.8618 Evaluate side-chains 146 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 2.031 ------------------------------------------------------------------------------- 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 162 optimal weight: 0.0270 chunk 145 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 174 optimal weight: 0.6980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 HIS A 515 GLN ** A 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 ASN A 914 HIS ** A1442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1555 GLN ** A1636 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15880 Z= 0.199 Angle : 0.656 9.270 21551 Z= 0.318 Chirality : 0.047 0.556 2461 Planarity : 0.004 0.065 2691 Dihedral : 14.209 151.343 2532 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.83 % Allowed : 9.95 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.20), residues: 1898 helix: 1.04 (0.17), residues: 995 sheet: -2.52 (0.40), residues: 156 loop : -2.27 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 782 HIS 0.014 0.001 HIS A 914 PHE 0.014 0.001 PHE A1811 TYR 0.017 0.001 TYR A1735 ARG 0.008 0.001 ARG A1860 *********************** 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 175 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 1.708 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 388 ARG cc_start: 0.7753 (tpt170) cc_final: 0.7532 (tpp-160) REVERT: A 442 PHE cc_start: 0.6198 (m-80) cc_final: 0.5146 (t80) REVERT: A 1041 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7163 (tp30) outliers start: 30 outliers final: 17 residues processed: 163 average time/residue: 0.2795 time to fit residues: 68.5634 Evaluate side-chains 156 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1158 THR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1479 TRP Chi-restraints excluded: chain A residue 1525 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 1857 VAL Chi-restraints excluded: chain A residue 1955 VAL Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2205 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 174 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 140 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 566 HIS ** A 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1636 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15880 Z= 0.216 Angle : 0.602 10.080 21551 Z= 0.294 Chirality : 0.045 0.518 2461 Planarity : 0.004 0.066 2691 Dihedral : 11.884 143.045 2532 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.07 % Allowed : 13.36 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1898 helix: 1.23 (0.17), residues: 1002 sheet: -2.40 (0.40), residues: 156 loop : -2.20 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 605 HIS 0.005 0.001 HIS A1625 PHE 0.012 0.001 PHE A1630 TYR 0.015 0.001 TYR A1735 ARG 0.005 0.000 ARG A 920 *********************** 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 179 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 145 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 388 ARG cc_start: 0.7787 (tpt170) cc_final: 0.7544 (tpp-160) REVERT: A 442 PHE cc_start: 0.6215 (m-80) cc_final: 0.5091 (t80) REVERT: A 1041 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7113 (tp30) REVERT: A 1479 TRP cc_start: 0.6386 (OUTLIER) cc_final: 0.2928 (p-90) outliers start: 34 outliers final: 23 residues processed: 166 average time/residue: 0.2920 time to fit residues: 72.4334 Evaluate side-chains 162 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1204 ASP 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 1612 GLU Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1818 ASN 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 1990 THR Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2143 MET Chi-restraints excluded: chain A residue 2197 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 0.9980 chunk 131 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 117 optimal weight: 0.0970 chunk 175 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 515 GLN ** A 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1555 GLN ** A1636 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15880 Z= 0.183 Angle : 0.575 10.891 21551 Z= 0.279 Chirality : 0.044 0.481 2461 Planarity : 0.004 0.065 2691 Dihedral : 10.908 136.782 2531 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.56 % Allowed : 14.70 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.20), residues: 1898 helix: 1.40 (0.17), residues: 996 sheet: -2.28 (0.40), residues: 159 loop : -2.15 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 605 HIS 0.003 0.001 HIS A1625 PHE 0.011 0.001 PHE A 713 TYR 0.014 0.001 TYR A1735 ARG 0.004 0.000 ARG A 920 *********************** 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 185 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 143 time to evaluate : 1.578 Fit side-chains revert: symmetry clash REVERT: A 388 ARG cc_start: 0.7798 (tpt170) cc_final: 0.7560 (tpp-160) REVERT: A 442 PHE cc_start: 0.6338 (m-80) cc_final: 0.5117 (t80) REVERT: A 1041 GLU cc_start: 0.7277 (mm-30) cc_final: 0.7053 (tp30) REVERT: A 1587 MET cc_start: 0.8275 (mpp) cc_final: 0.8002 (mpp) REVERT: A 1899 HIS cc_start: 0.5528 (OUTLIER) cc_final: 0.4830 (t-90) outliers start: 42 outliers final: 28 residues processed: 170 average time/residue: 0.3002 time to fit residues: 78.0694 Evaluate side-chains 165 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1204 ASP 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 1612 GLU Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1821 THR Chi-restraints excluded: chain A residue 1857 VAL Chi-restraints excluded: chain A residue 1899 HIS Chi-restraints excluded: chain A residue 1990 THR Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2143 MET Chi-restraints excluded: chain A residue 2169 MET Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2205 MET Chi-restraints excluded: chain A residue 2237 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 10.0000 chunk 105 optimal weight: 0.0970 chunk 2 optimal weight: 0.6980 chunk 138 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 128 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 166 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 515 GLN A 823 ASN ** A 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1442 ASN A1636 ASN ** A1799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1899 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15880 Z= 0.172 Angle : 0.549 10.343 21551 Z= 0.267 Chirality : 0.043 0.462 2461 Planarity : 0.004 0.064 2691 Dihedral : 10.129 131.800 2531 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.11 % Allowed : 14.95 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.20), residues: 1898 helix: 1.46 (0.17), residues: 1003 sheet: -2.24 (0.40), residues: 159 loop : -2.08 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 605 HIS 0.002 0.001 HIS A1625 PHE 0.022 0.001 PHE A 812 TYR 0.013 0.001 TYR A1735 ARG 0.004 0.000 ARG A1830 *********************** 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 202 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 151 time to evaluate : 1.704 Fit side-chains revert: symmetry clash REVERT: A 388 ARG cc_start: 0.7782 (tpt170) cc_final: 0.7555 (tpp-160) REVERT: A 442 PHE cc_start: 0.6361 (m-80) cc_final: 0.5107 (t80) REVERT: A 1041 GLU cc_start: 0.7227 (mm-30) cc_final: 0.7021 (tp30) REVERT: A 1551 TRP cc_start: 0.8446 (p90) cc_final: 0.8234 (p90) REVERT: A 1587 MET cc_start: 0.8363 (mpp) cc_final: 0.8020 (mpp) REVERT: A 1899 HIS cc_start: 0.5738 (OUTLIER) cc_final: 0.5045 (t70) outliers start: 51 outliers final: 31 residues processed: 186 average time/residue: 0.2850 time to fit residues: 80.1628 Evaluate side-chains 172 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1204 ASP Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1394 ILE Chi-restraints excluded: chain A residue 1442 ASN 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 1612 GLU Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1818 ASN 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 1899 HIS Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2092 VAL Chi-restraints excluded: chain A residue 2143 MET Chi-restraints excluded: chain A residue 2168 THR Chi-restraints excluded: chain A residue 2169 MET Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2205 MET Chi-restraints excluded: chain A residue 2237 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.5980 chunk 167 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 185 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 86 optimal weight: 0.0470 chunk 15 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 GLN ** A 823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1899 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15880 Z= 0.172 Angle : 0.537 8.944 21551 Z= 0.264 Chirality : 0.043 0.449 2461 Planarity : 0.004 0.063 2691 Dihedral : 9.694 128.788 2531 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.81 % Allowed : 16.17 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1898 helix: 1.56 (0.17), residues: 997 sheet: -2.21 (0.40), residues: 162 loop : -2.04 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 605 HIS 0.005 0.001 HIS A1899 PHE 0.032 0.001 PHE A 812 TYR 0.016 0.001 TYR A 106 ARG 0.007 0.000 ARG A 920 *********************** 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 187 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 141 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 388 ARG cc_start: 0.7773 (tpt170) cc_final: 0.7555 (tpp-160) REVERT: A 442 PHE cc_start: 0.6315 (m-80) cc_final: 0.5049 (t80) REVERT: A 1041 GLU cc_start: 0.7227 (mm-30) cc_final: 0.7020 (tp30) REVERT: A 1551 TRP cc_start: 0.8408 (p90) cc_final: 0.8194 (p90) outliers start: 46 outliers final: 35 residues processed: 173 average time/residue: 0.2947 time to fit residues: 78.0086 Evaluate side-chains 172 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 137 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 576 ASP 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 1012 ASN Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1204 ASP 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 1480 THR Chi-restraints excluded: chain A residue 1498 MET Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1818 ASN Chi-restraints excluded: chain A residue 1821 THR Chi-restraints excluded: chain A residue 1830 ARG Chi-restraints excluded: chain A residue 1990 THR Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2143 MET Chi-restraints excluded: chain A residue 2168 THR Chi-restraints excluded: chain A residue 2169 MET Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2205 MET Chi-restraints excluded: chain A residue 2237 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 185 optimal weight: 0.4980 chunk 115 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 823 ASN ** A 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1799 ASN A1899 HIS ** A1974 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 15880 Z= 0.462 Angle : 0.688 9.027 21551 Z= 0.345 Chirality : 0.049 0.534 2461 Planarity : 0.005 0.070 2691 Dihedral : 9.982 125.294 2531 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 3.23 % Allowed : 17.88 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.20), residues: 1898 helix: 1.10 (0.17), residues: 1008 sheet: -2.65 (0.37), residues: 174 loop : -2.25 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1479 HIS 0.006 0.001 HIS A1625 PHE 0.020 0.002 PHE A 718 TYR 0.022 0.002 TYR A2071 ARG 0.007 0.000 ARG A 920 *********************** 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 194 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 141 time to evaluate : 1.713 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 1041 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7084 (tp30) REVERT: A 1665 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8419 (ttpt) outliers start: 53 outliers final: 39 residues processed: 180 average time/residue: 0.2760 time to fit residues: 76.1428 Evaluate side-chains 172 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 132 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 717 ILE Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 951 ILE Chi-restraints excluded: chain A residue 1012 ASN Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1204 ASP 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 1519 THR Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1665 LYS Chi-restraints excluded: chain A residue 1698 VAL Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1800 LEU Chi-restraints excluded: chain A residue 1818 ASN 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 2021 ASP Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2070 THR Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2123 VAL Chi-restraints excluded: chain A residue 2168 THR Chi-restraints excluded: chain A residue 2169 MET Chi-restraints excluded: chain A residue 2197 VAL Chi-restraints excluded: chain A residue 2237 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 168 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 HIS ** A 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15880 Z= 0.221 Angle : 0.585 10.646 21551 Z= 0.287 Chirality : 0.044 0.472 2461 Planarity : 0.004 0.066 2691 Dihedral : 9.485 121.021 2531 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.50 % Allowed : 18.67 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.20), residues: 1898 helix: 1.33 (0.17), residues: 1008 sheet: -2.53 (0.38), residues: 161 loop : -2.19 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 605 HIS 0.011 0.001 HIS A1899 PHE 0.023 0.001 PHE A1900 TYR 0.013 0.001 TYR A1735 ARG 0.018 0.000 ARG A1898 *********************** 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 182 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 141 time to evaluate : 1.926 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 1041 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7028 (tp30) outliers start: 41 outliers final: 36 residues processed: 170 average time/residue: 0.3549 time to fit residues: 93.0296 Evaluate side-chains 176 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 140 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU 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 505 ILE Chi-restraints excluded: chain A residue 576 ASP 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 1012 ASN Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1204 ASP 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 1535 VAL Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1818 ASN Chi-restraints excluded: chain A residue 1821 THR Chi-restraints excluded: chain A residue 1830 ARG Chi-restraints excluded: chain A residue 1990 THR Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2168 THR Chi-restraints excluded: chain A residue 2169 MET 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 177 optimal weight: 0.8980 chunk 161 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 163 optimal weight: 0.6980 chunk 171 optimal weight: 0.2980 chunk 113 optimal weight: 0.0770 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1477 GLN ** A1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1899 HIS ** A2075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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 : 0.003 0.041 15880 Z= 0.173 Angle : 0.562 9.787 21551 Z= 0.273 Chirality : 0.043 0.448 2461 Planarity : 0.004 0.063 2691 Dihedral : 9.079 118.180 2531 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.68 % Allowed : 18.30 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.20), residues: 1898 helix: 1.48 (0.17), residues: 1007 sheet: -2.49 (0.37), residues: 172 loop : -2.08 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 605 HIS 0.003 0.001 HIS A 566 PHE 0.016 0.001 PHE A 718 TYR 0.013 0.001 TYR A1735 ARG 0.005 0.000 ARG A 920 *********************** 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 185 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 141 time to evaluate : 1.734 Fit side-chains revert: symmetry clash REVERT: A 395 MET cc_start: 0.8138 (mtt) cc_final: 0.7890 (mtp) REVERT: A 1041 GLU cc_start: 0.7318 (mm-30) cc_final: 0.7051 (tp30) REVERT: A 1220 LYS cc_start: 0.8119 (mtmm) cc_final: 0.7829 (mtpt) REVERT: A 1665 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8306 (ttpt) REVERT: A 2183 ASN cc_start: 0.8593 (t0) cc_final: 0.8352 (t0) outliers start: 44 outliers final: 37 residues processed: 173 average time/residue: 0.2607 time to fit residues: 69.5825 Evaluate side-chains 177 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 139 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 576 ASP 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 1012 ASN Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1204 ASP 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 1535 VAL Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1665 LYS Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1818 ASN Chi-restraints excluded: chain A residue 1821 THR Chi-restraints excluded: chain A residue 1830 ARG Chi-restraints excluded: chain A residue 1899 HIS Chi-restraints excluded: chain A residue 1990 THR Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2070 THR Chi-restraints excluded: chain A residue 2085 LEU 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 182 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 126 optimal weight: 9.9990 chunk 191 optimal weight: 0.7980 chunk 176 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 117 optimal weight: 0.2980 chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1899 HIS ** A2075 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15880 Z= 0.167 Angle : 0.553 9.653 21551 Z= 0.269 Chirality : 0.043 0.446 2461 Planarity : 0.004 0.061 2691 Dihedral : 8.817 116.130 2531 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.68 % Allowed : 18.43 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1898 helix: 1.54 (0.17), residues: 1008 sheet: -2.29 (0.39), residues: 162 loop : -2.06 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 605 HIS 0.003 0.001 HIS A 566 PHE 0.045 0.001 PHE A1900 TYR 0.013 0.001 TYR A1735 ARG 0.005 0.000 ARG A 920 ********************** 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 188 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 144 time to evaluate : 1.780 Fit side-chains revert: symmetry clash REVERT: A 109 PHE cc_start: 0.8648 (t80) cc_final: 0.8444 (t80) REVERT: A 395 MET cc_start: 0.7956 (mtt) cc_final: 0.7701 (mtp) REVERT: A 1041 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7110 (tp30) REVERT: A 1220 LYS cc_start: 0.8124 (mtmm) cc_final: 0.7846 (mtpt) REVERT: A 1665 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8462 (ttpt) REVERT: A 2183 ASN cc_start: 0.8628 (t0) cc_final: 0.8349 (t0) outliers start: 44 outliers final: 36 residues processed: 178 average time/residue: 0.2681 time to fit residues: 73.5260 Evaluate side-chains 179 residues out of total 1690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 142 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 505 ILE 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 1012 ASN Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1158 THR Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1204 ASP 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 1535 VAL Chi-restraints excluded: chain A residue 1612 GLU Chi-restraints excluded: chain A residue 1665 LYS Chi-restraints excluded: chain A residue 1698 VAL Chi-restraints excluded: chain A residue 1718 VAL Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1818 ASN Chi-restraints excluded: chain A residue 1821 THR Chi-restraints excluded: chain A residue 1830 ARG Chi-restraints excluded: chain A residue 1899 HIS Chi-restraints excluded: chain A residue 1990 THR Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2061 THR Chi-restraints excluded: chain A residue 2085 LEU 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 162 optimal weight: 0.2980 chunk 46 optimal weight: 0.7980 chunk 140 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 156 optimal weight: 0.6980 chunk 19 optimal weight: 0.0470 chunk 28 optimal weight: 10.0000 chunk 133 optimal weight: 0.0060 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 HIS ** A 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1899 HIS ** A2075 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 = 0.3782 r_free = 0.3782 target = 0.140411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.110605 restraints weight = 21171.882| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.20 r_work: 0.3228 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15880 Z= 0.147 Angle : 0.544 9.383 21551 Z= 0.263 Chirality : 0.042 0.434 2461 Planarity : 0.004 0.062 2691 Dihedral : 8.568 113.847 2531 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.32 % Allowed : 18.91 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 1898 helix: 1.64 (0.17), residues: 1002 sheet: -2.16 (0.39), residues: 162 loop : -1.96 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 605 HIS 0.011 0.001 HIS A1899 PHE 0.040 0.001 PHE A1900 TYR 0.013 0.001 TYR A1735 ARG 0.005 0.000 ARG A 920 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3231.64 seconds wall clock time: 59 minutes 37.53 seconds (3577.53 seconds total)