Starting phenix.real_space_refine on Wed Mar 4 22:39:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pw9_13679/03_2026/7pw9_13679.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pw9_13679/03_2026/7pw9_13679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pw9_13679/03_2026/7pw9_13679.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pw9_13679/03_2026/7pw9_13679.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pw9_13679/03_2026/7pw9_13679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pw9_13679/03_2026/7pw9_13679.map" } resolution = 3.12 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= 0.003 sd= 0.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 1 5.21 5 S 80 5.16 5 C 10472 2.51 5 N 2882 2.21 5 O 2892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 16339 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1298, 9205 Classifications: {'peptide': 1298} Incomplete info: {'truncation_to_alanine': 334} Link IDs: {'PTRANS': 35, 'TRANS': 1262} Chain breaks: 25 Unresolved non-hydrogen bonds: 921 Unresolved non-hydrogen angles: 1205 Unresolved non-hydrogen dihedrals: 669 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'UNK:plan-1': 121, 'PHE:plan': 5, 'ASN:plan1': 13, 'ARG:plan': 6, 'ASP:plan': 30, 'GLN:plan1': 9, 'TRP:plan': 2, 'GLU:plan': 44, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 559 Chain: "A" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1457 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain breaks: 5 Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'UNK:plan-1': 42, 'GLU:plan': 7, 'ARG:plan': 2, 'ASP:plan': 6, 'GLN:plan1': 7, 'ASN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 141 Chain: "A" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 202 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'UNK:plan-1': 16, 'GLU:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2967 Classifications: {'peptide': 398} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 19, 'TRANS': 378} Chain breaks: 3 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'UNK:plan-1': 16, 'ARG:plan': 3, 'GLU:plan': 16, 'ASN:plan1': 1, 'ASP:plan': 8, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 130 Chain: "C" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2409 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 292} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 7, 'ARG:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 72 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'ANP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C1 IHP A3702 " occ=0.00 ... (34 atoms not shown) pdb=" P6 IHP A3702 " occ=0.00 residue: pdb="MG MG C 602 " occ=0.00 Time building chain proxies: 3.20, per 1000 atoms: 0.20 Number of scatterers: 16339 At special positions: 0 Unit cell: (131.085, 114.061, 180.454, 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 80 16.00 P 12 15.00 Mg 1 11.99 O 2892 8.00 N 2882 7.00 C 10472 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 672.6 milliseconds 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4362 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 4 sheets defined 78.1% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 147 through 156 removed outlier: 3.884A pdb=" N UNK A 154 " --> pdb=" O UNK A 150 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N UNK A 155 " --> pdb=" O UNK A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 175 removed outlier: 3.888A pdb=" N UNK A 172 " --> pdb=" O UNK A 168 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N UNK A 173 " --> pdb=" O UNK A 169 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N UNK A 175 " --> pdb=" O UNK A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 199 removed outlier: 3.506A pdb=" N UNK A 199 " --> pdb=" O UNK A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 219 Processing helix chain 'A' and resid 230 through 244 Processing helix chain 'A' and resid 249 through 265 removed outlier: 4.067A pdb=" N UNK A 265 " --> pdb=" O UNK A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 Processing helix chain 'A' and resid 291 through 303 removed outlier: 3.779A pdb=" N UNK A 303 " --> pdb=" O UNK A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 323 removed outlier: 3.605A pdb=" N THR A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 347 removed outlier: 3.646A pdb=" N VAL A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 376 removed outlier: 3.611A pdb=" N GLN A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 411 Processing helix chain 'A' and resid 429 through 444 Processing helix chain 'A' and resid 449 through 467 removed outlier: 3.642A pdb=" N LEU A 453 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 488 removed outlier: 4.382A pdb=" N VAL A 478 " --> pdb=" O HIS A 474 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 511 Processing helix chain 'A' and resid 516 through 524 removed outlier: 3.688A pdb=" N VAL A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 534 removed outlier: 3.998A pdb=" N PHE A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 554 removed outlier: 3.928A pdb=" N VAL A 542 " --> pdb=" O GLU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 582 removed outlier: 4.239A pdb=" N THR A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA A 564 " --> pdb=" O VAL A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.548A pdb=" N PHE A 597 " --> pdb=" O HIS A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 623 removed outlier: 3.958A pdb=" N THR A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 644 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.799A pdb=" N HIS A 656 " --> pdb=" O ASP A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 675 removed outlier: 4.075A pdb=" N GLN A 661 " --> pdb=" O PHE A 657 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N HIS A 675 " --> pdb=" O HIS A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 679 Processing helix chain 'A' and resid 699 through 704 Processing helix chain 'A' and resid 706 through 719 Processing helix chain 'A' and resid 724 through 742 Processing helix chain 'A' and resid 743 through 744 No H-bonds generated for 'chain 'A' and resid 743 through 744' Processing helix chain 'A' and resid 745 through 753 removed outlier: 3.586A pdb=" N TYR A 748 " --> pdb=" O SER A 745 " (cutoff:3.500A) Proline residue: A 750 - end of helix Processing helix chain 'A' and resid 754 through 768 removed outlier: 3.513A pdb=" N HIS A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 768 " --> pdb=" O LEU A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 786 removed outlier: 3.731A pdb=" N CYS A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 786 " --> pdb=" O SER A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 806 removed outlier: 3.860A pdb=" N ARG A 797 " --> pdb=" O ASP A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 824 removed outlier: 3.561A pdb=" N ARG A 814 " --> pdb=" O GLY A 810 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 819 " --> pdb=" O GLN A 815 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 835 through 851 Processing helix chain 'A' and resid 858 through 872 Processing helix chain 'A' and resid 882 through 890 removed outlier: 3.561A pdb=" N LEU A 886 " --> pdb=" O TRP A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 906 Processing helix chain 'A' and resid 908 through 927 Processing helix chain 'A' and resid 937 through 956 removed outlier: 3.672A pdb=" N ASN A 956 " --> pdb=" O ALA A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 999 removed outlier: 3.933A pdb=" N HIS A 973 " --> pdb=" O ASN A 969 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 974 " --> pdb=" O ASP A 970 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 984 " --> pdb=" O LEU A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1019 removed outlier: 3.509A pdb=" N PHE A1015 " --> pdb=" O VAL A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1041 removed outlier: 3.572A pdb=" N CYS A1023 " --> pdb=" O ASN A1019 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU A1032 " --> pdb=" O THR A1028 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER A1033 " --> pdb=" O ARG A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1058 removed outlier: 3.739A pdb=" N THR A1047 " --> pdb=" O GLN A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1083 removed outlier: 3.779A pdb=" N THR A1072 " --> pdb=" O GLU A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1097 Processing helix chain 'A' and resid 1105 through 1115 removed outlier: 3.825A pdb=" N SER A1109 " --> pdb=" O LEU A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1134 removed outlier: 3.566A pdb=" N VAL A1123 " --> pdb=" O GLU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1151 removed outlier: 3.637A pdb=" N LEU A1149 " --> pdb=" O SER A1145 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A1151 " --> pdb=" O LEU A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1197 removed outlier: 3.692A pdb=" N ILE A1197 " --> pdb=" O CYS A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1216 Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.532A pdb=" N ILE A1231 " --> pdb=" O ASP A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1250 Processing helix chain 'A' and resid 1281 through 1305 Processing helix chain 'A' and resid 1319 through 1332 Processing helix chain 'A' and resid 1332 through 1341 removed outlier: 3.688A pdb=" N THR A1341 " --> pdb=" O LEU A1337 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1367 Processing helix chain 'A' and resid 1370 through 1374 Processing helix chain 'A' and resid 1378 through 1384 Processing helix chain 'A' and resid 1390 through 1407 removed outlier: 3.969A pdb=" N TYR A1402 " --> pdb=" O ARG A1398 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN A1403 " --> pdb=" O TYR A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1410 No H-bonds generated for 'chain 'A' and resid 1408 through 1410' Processing helix chain 'A' and resid 1417 through 1435 removed outlier: 3.546A pdb=" N ARG A1435 " --> pdb=" O PHE A1431 " (cutoff:3.500A) Processing helix chain 'A' and resid 1437 through 1450 Processing helix chain 'A' and resid 1458 through 1467 removed outlier: 3.786A pdb=" N LEU A1462 " --> pdb=" O THR A1458 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A1463 " --> pdb=" O ALA A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1495 Processing helix chain 'A' and resid 1496 through 1513 removed outlier: 3.737A pdb=" N LYS A1513 " --> pdb=" O ILE A1509 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1535 removed outlier: 4.349A pdb=" N ALA A1522 " --> pdb=" O GLU A1518 " (cutoff:3.500A) Processing helix chain 'A' and resid 1539 through 1551 Processing helix chain 'A' and resid 1559 through 1570 Processing helix chain 'A' and resid 1586 through 1591 Processing helix chain 'A' and resid 1595 through 1612 removed outlier: 3.928A pdb=" N ILE A1600 " --> pdb=" O GLU A1596 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A1601 " --> pdb=" O PRO A1597 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY A1602 " --> pdb=" O ASP A1598 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1637 removed outlier: 3.801A pdb=" N TRP A1619 " --> pdb=" O VAL A1615 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A1632 " --> pdb=" O ARG A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1656 Processing helix chain 'A' and resid 1664 through 1674 removed outlier: 3.716A pdb=" N UNK A1674 " --> pdb=" O UNK A1670 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1716 Processing helix chain 'A' and resid 1728 through 1741 removed outlier: 3.627A pdb=" N PHE A1741 " --> pdb=" O VAL A1737 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1758 Processing helix chain 'A' and resid 1781 through 1799 removed outlier: 3.519A pdb=" N ILE A1785 " --> pdb=" O THR A1781 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1811 removed outlier: 3.628A pdb=" N LEU A1807 " --> pdb=" O LEU A1803 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N HIS A1809 " --> pdb=" O GLN A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1822 through 1829 Processing helix chain 'A' and resid 1830 through 1832 No H-bonds generated for 'chain 'A' and resid 1830 through 1832' Processing helix chain 'A' and resid 1835 through 1850 removed outlier: 3.606A pdb=" N GLN A1850 " --> pdb=" O CYS A1846 " (cutoff:3.500A) Processing helix chain 'A' and resid 1852 through 1856 removed outlier: 3.813A pdb=" N LEU A1855 " --> pdb=" O SER A1852 " (cutoff:3.500A) Processing helix chain 'A' and resid 1857 through 1865 Processing helix chain 'A' and resid 1924 through 1939 removed outlier: 3.689A pdb=" N CYS A1929 " --> pdb=" O MET A1925 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TYR A1930 " --> pdb=" O MET A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1960 removed outlier: 4.535A pdb=" N VAL A1960 " --> pdb=" O ARG A1956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1961 through 1978 removed outlier: 4.386A pdb=" N LEU A1978 " --> pdb=" O HIS A1974 " (cutoff:3.500A) Processing helix chain 'A' and resid 2007 through 2020 Processing helix chain 'A' and resid 2036 through 2044 Processing helix chain 'A' and resid 2046 through 2056 removed outlier: 4.201A pdb=" N LYS A2056 " --> pdb=" O LEU A2052 " (cutoff:3.500A) Processing helix chain 'A' and resid 2069 through 2083 removed outlier: 3.830A pdb=" N UNK A2083 " --> pdb=" O UNK A2079 " (cutoff:3.500A) Processing helix chain 'A' and resid 2092 through 2096 Processing helix chain 'A' and resid 2160 through 2176 removed outlier: 3.585A pdb=" N GLU A2164 " --> pdb=" O LEU A2160 " (cutoff:3.500A) Processing helix chain 'A' and resid 2177 through 2178 No H-bonds generated for 'chain 'A' and resid 2177 through 2178' Processing helix chain 'A' and resid 2179 through 2184 removed outlier: 4.178A pdb=" N GLU A2184 " --> pdb=" O ASN A2181 " (cutoff:3.500A) Processing helix chain 'A' and resid 2214 through 2232 removed outlier: 3.508A pdb=" N TYR A2218 " --> pdb=" O LEU A2214 " (cutoff:3.500A) Processing helix chain 'A' and resid 2248 through 2263 Proline residue: A2259 - end of helix Processing helix chain 'A' and resid 2276 through 2291 removed outlier: 3.522A pdb=" N MET A2280 " --> pdb=" O PRO A2276 " (cutoff:3.500A) Processing helix chain 'A' and resid 2294 through 2304 removed outlier: 3.560A pdb=" N GLU A2299 " --> pdb=" O LEU A2295 " (cutoff:3.500A) Processing helix chain 'A' and resid 2306 through 2332 Processing helix chain 'A' and resid 2337 through 2339 No H-bonds generated for 'chain 'A' and resid 2337 through 2339' Processing helix chain 'A' and resid 2360 through 2364 removed outlier: 3.562A pdb=" N SER A2364 " --> pdb=" O LYS A2361 " (cutoff:3.500A) Processing helix chain 'A' and resid 2376 through 2382 Processing helix chain 'A' and resid 2390 through 2406 Processing helix chain 'A' and resid 2406 through 2419 removed outlier: 3.846A pdb=" N LEU A2410 " --> pdb=" O GLY A2406 " (cutoff:3.500A) Processing helix chain 'A' and resid 3608 through 3622 Processing helix chain 'A' and resid 3632 through 3646 Processing helix chain 'A' and resid 3646 through 3652 removed outlier: 3.656A pdb=" N GLN A3652 " --> pdb=" O ASP A3648 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 198 Processing helix chain 'C' and resid 216 through 226 Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.600A pdb=" N TYR C 236 " --> pdb=" O GLN C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 removed outlier: 4.104A pdb=" N GLU C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 284 removed outlier: 3.513A pdb=" N LEU C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN C 284 " --> pdb=" O ASP C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 315 removed outlier: 3.561A pdb=" N TYR C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 338 Processing helix chain 'C' and resid 380 through 395 Processing helix chain 'C' and resid 408 through 412 Processing helix chain 'C' and resid 465 through 479 Processing helix chain 'C' and resid 491 through 508 Processing helix chain 'C' and resid 510 through 519 removed outlier: 3.506A pdb=" N LEU C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2090 through 2091 removed outlier: 7.470A pdb=" N THR A2127 " --> pdb=" O LEU A2141 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU A2141 " --> pdb=" O THR A2127 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU A2141 " --> pdb=" O VAL A2124 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL A2124 " --> pdb=" O LEU A2141 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU A2143 " --> pdb=" O HIS A2122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2090 through 2091 removed outlier: 7.470A pdb=" N THR A2127 " --> pdb=" O LEU A2141 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU A2141 " --> pdb=" O THR A2127 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A2138 " --> pdb=" O PHE A2154 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2212 through 2213 Processing sheet with id=AA4, first strand: chain 'C' and resid 181 through 184 removed outlier: 6.421A pdb=" N ILE C 256 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP C 269 " --> pdb=" O ASP C 257 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU C 205 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU C 268 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL C 207 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR C 270 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VAL C 209 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL C 206 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE C 319 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY C 208 " --> pdb=" O ILE C 319 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL C 321 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU C 210 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N PHE C 429 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE C 369 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL C 431 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLN C 371 " --> pdb=" O VAL C 431 " (cutoff:3.500A) 1075 hydrogen bonds defined for protein. 3141 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: 3.00 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2561 1.30 - 1.43: 4216 1.43 - 1.56: 9714 1.56 - 1.69: 17 1.69 - 1.81: 126 Bond restraints: 16634 Sorted by residual: bond pdb=" O3A ANP A3701 " pdb=" PB ANP A3701 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" CA LEU A 741 " pdb=" C LEU A 741 " ideal model delta sigma weight residual 1.522 1.440 0.082 1.39e-02 5.18e+03 3.50e+01 bond pdb=" N3B ANP A3701 " pdb=" PG ANP A3701 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C LEU A 741 " pdb=" O LEU A 741 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.32e-02 5.74e+03 1.95e+01 bond pdb=" C MET A 742 " pdb=" O MET A 742 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.35e-02 5.49e+03 1.69e+01 ... (remaining 16629 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 22597 3.31 - 6.61: 116 6.61 - 9.92: 22 9.92 - 13.23: 2 13.23 - 16.53: 1 Bond angle restraints: 22738 Sorted by residual: angle pdb=" PB ANP A3701 " pdb=" N3B ANP A3701 " pdb=" PG ANP A3701 " ideal model delta sigma weight residual 126.95 110.42 16.53 3.00e+00 1.11e-01 3.04e+01 angle pdb=" N LYS A 744 " pdb=" CA LYS A 744 " pdb=" C LYS A 744 " ideal model delta sigma weight residual 111.28 115.80 -4.52 1.09e+00 8.42e-01 1.72e+01 angle pdb=" N THR A 747 " pdb=" CA THR A 747 " pdb=" C THR A 747 " ideal model delta sigma weight residual 111.75 116.59 -4.84 1.28e+00 6.10e-01 1.43e+01 angle pdb=" O1B ANP A3701 " pdb=" PB ANP A3701 " pdb=" O2B ANP A3701 " ideal model delta sigma weight residual 120.08 109.11 10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" N ILE A2353 " pdb=" CA ILE A2353 " pdb=" C ILE A2353 " ideal model delta sigma weight residual 109.34 116.31 -6.97 2.08e+00 2.31e-01 1.12e+01 ... (remaining 22733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.40: 9676 33.40 - 66.80: 221 66.80 - 100.19: 19 100.19 - 133.59: 8 133.59 - 166.99: 3 Dihedral angle restraints: 9927 sinusoidal: 3286 harmonic: 6641 Sorted by residual: dihedral pdb=" C6 IHP A3702 " pdb=" C1 IHP A3702 " pdb=" C2 IHP A3702 " pdb=" O12 IHP A3702 " ideal model delta sinusoidal sigma weight residual 61.05 -105.94 166.99 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C4 IHP A3702 " pdb=" C2 IHP A3702 " pdb=" C3 IHP A3702 " pdb=" O12 IHP A3702 " ideal model delta sinusoidal sigma weight residual 60.90 -157.33 -141.77 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" O12 IHP A3702 " pdb=" C2 IHP A3702 " pdb=" C3 IHP A3702 " pdb=" O13 IHP A3702 " ideal model delta sinusoidal sigma weight residual 64.08 -73.04 137.12 1 3.00e+01 1.11e-03 1.85e+01 ... (remaining 9924 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.003: 2804 1.003 - 2.005: 0 2.005 - 3.008: 0 3.008 - 4.011: 0 4.011 - 5.013: 3 Chirality restraints: 2807 Sorted by residual: chirality pdb=" C2 IHP A3702 " pdb=" C1 IHP A3702 " pdb=" C3 IHP A3702 " pdb=" O12 IHP A3702 " both_signs ideal model delta sigma weight residual False -2.52 2.49 -5.01 2.00e-01 2.50e+01 6.28e+02 chirality pdb=" C4 IHP A3702 " pdb=" C3 IHP A3702 " pdb=" C5 IHP A3702 " pdb=" O14 IHP A3702 " both_signs ideal model delta sigma weight residual False 2.48 -2.41 4.89 2.00e-01 2.50e+01 5.98e+02 chirality pdb=" C1 IHP A3702 " pdb=" C2 IHP A3702 " pdb=" C6 IHP A3702 " pdb=" O11 IHP A3702 " both_signs ideal model delta sigma weight residual False 2.32 -2.45 4.76 2.00e-01 2.50e+01 5.68e+02 ... (remaining 2804 not shown) Planarity restraints: 2823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A2258 " 0.031 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO A2259 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A2259 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A2259 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 740 " -0.010 2.00e-02 2.50e+03 1.90e-02 3.60e+00 pdb=" C VAL A 740 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL A 740 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 741 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 742 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C MET A 742 " 0.033 2.00e-02 2.50e+03 pdb=" O MET A 742 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG A 743 " -0.011 2.00e-02 2.50e+03 ... (remaining 2820 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 83 2.60 - 3.17: 13713 3.17 - 3.75: 24949 3.75 - 4.32: 31557 4.32 - 4.90: 54761 Nonbonded interactions: 125063 Sorted by model distance: nonbonded pdb=" O1G ATP C 601 " pdb="MG MG C 602 " model vdw 2.021 2.170 nonbonded pdb=" O1A ATP C 601 " pdb="MG MG C 602 " model vdw 2.021 2.170 nonbonded pdb=" O3B ATP C 601 " pdb="MG MG C 602 " model vdw 2.029 2.170 nonbonded pdb=" O3A ATP C 601 " pdb="MG MG C 602 " model vdw 2.059 2.170 nonbonded pdb=" O TYR A 888 " pdb=" OG SER C 479 " model vdw 2.177 3.040 ... (remaining 125058 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.350 Find NCS groups from input model: 0.080 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 : 0.004 0.142 16635 Z= 0.190 Angle : 0.672 16.532 22738 Z= 0.350 Chirality : 0.165 5.013 2807 Planarity : 0.004 0.048 2823 Dihedral : 15.149 166.991 5565 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.34 % Favored : 96.61 % Rotamer: Outliers : 0.07 % Allowed : 0.41 % Favored : 99.53 % 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: 1.77 (0.20), residues: 2008 helix: 2.49 (0.15), residues: 1281 sheet: -0.65 (0.53), residues: 81 loop : -1.42 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 743 TYR 0.018 0.001 TYR C 299 PHE 0.013 0.001 PHE C 466 TRP 0.026 0.001 TRP A1629 HIS 0.003 0.001 HIS A2352 Details of bonding type rmsd covalent geometry : bond 0.00353 (16634) covalent geometry : angle 0.67227 (22738) hydrogen bonds : bond 0.13809 ( 1071) hydrogen bonds : angle 4.41657 ( 3141) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.571 Fit side-chains REVERT: A 368 MET cc_start: 0.5259 (ptm) cc_final: 0.4672 (tmm) REVERT: A 1857 LEU cc_start: 0.8295 (tp) cc_final: 0.8030 (tp) REVERT: A 2326 MET cc_start: 0.8672 (mmp) cc_final: 0.8317 (mmp) REVERT: A 2345 MET cc_start: 0.8110 (mmt) cc_final: 0.7881 (mmt) outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 0.1177 time to fit residues: 35.1744 Evaluate side-chains 160 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 741 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 212 optimal weight: 0.2980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1344 GLN C 233 GLN C 322 GLN C 397 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.179384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.142159 restraints weight = 22306.518| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.81 r_work: 0.3508 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16635 Z= 0.168 Angle : 0.575 11.117 22738 Z= 0.281 Chirality : 0.040 0.339 2807 Planarity : 0.004 0.047 2823 Dihedral : 9.513 114.498 2475 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.88 % Favored : 96.07 % Rotamer: Outliers : 1.02 % Allowed : 7.99 % Favored : 91.00 % 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: 1.75 (0.20), residues: 2008 helix: 2.44 (0.15), residues: 1296 sheet: -0.28 (0.57), residues: 81 loop : -1.49 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2336 TYR 0.025 0.001 TYR A 998 PHE 0.015 0.002 PHE A 760 TRP 0.018 0.002 TRP A3657 HIS 0.011 0.001 HIS C 397 Details of bonding type rmsd covalent geometry : bond 0.00407 (16634) covalent geometry : angle 0.57504 (22738) hydrogen bonds : bond 0.04950 ( 1071) hydrogen bonds : angle 3.62541 ( 3141) Misc. bond : bond 0.00092 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.474 Fit side-chains REVERT: A 368 MET cc_start: 0.6525 (ptm) cc_final: 0.5703 (tmm) REVERT: A 719 LYS cc_start: 0.8557 (mttt) cc_final: 0.8331 (mttp) REVERT: A 1744 TYR cc_start: 0.7728 (m-10) cc_final: 0.7520 (m-80) REVERT: A 1949 GLN cc_start: 0.7925 (mt0) cc_final: 0.7705 (mt0) REVERT: A 2345 MET cc_start: 0.8585 (mmt) cc_final: 0.8305 (mmt) outliers start: 15 outliers final: 11 residues processed: 169 average time/residue: 0.1089 time to fit residues: 29.1675 Evaluate side-chains 160 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 1512 CYS Chi-restraints excluded: chain A residue 1565 ILE Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1598 ASP Chi-restraints excluded: chain A residue 1634 VAL Chi-restraints excluded: chain A residue 1835 VAL Chi-restraints excluded: chain A residue 1836 TYR Chi-restraints excluded: chain C residue 427 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 116 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 7 optimal weight: 30.0000 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 128 optimal weight: 4.9990 chunk 94 optimal weight: 0.0470 chunk 146 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 233 GLN C 372 ASN C 397 HIS C 399 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.179008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.141192 restraints weight = 22737.044| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.27 r_work: 0.3498 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16635 Z= 0.148 Angle : 0.536 11.087 22738 Z= 0.262 Chirality : 0.039 0.325 2807 Planarity : 0.004 0.045 2823 Dihedral : 9.041 109.790 2473 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.49 % Favored : 96.46 % Rotamer: Outliers : 1.15 % Allowed : 11.04 % Favored : 87.81 % 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: 1.70 (0.20), residues: 2008 helix: 2.42 (0.15), residues: 1304 sheet: -0.18 (0.59), residues: 81 loop : -1.63 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2336 TYR 0.022 0.001 TYR A 998 PHE 0.013 0.001 PHE A1431 TRP 0.017 0.001 TRP A3657 HIS 0.006 0.001 HIS C 397 Details of bonding type rmsd covalent geometry : bond 0.00359 (16634) covalent geometry : angle 0.53550 (22738) hydrogen bonds : bond 0.04582 ( 1071) hydrogen bonds : angle 3.46799 ( 3141) Misc. bond : bond 0.00079 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 1352 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8166 (tt) REVERT: A 2345 MET cc_start: 0.8588 (mmt) cc_final: 0.8287 (mmt) REVERT: C 492 GLU cc_start: 0.8239 (mt-10) cc_final: 0.8020 (mt-10) outliers start: 17 outliers final: 11 residues processed: 170 average time/residue: 0.1082 time to fit residues: 29.3338 Evaluate side-chains 159 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1512 CYS Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1598 ASP Chi-restraints excluded: chain A residue 1634 VAL Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1836 TYR Chi-restraints excluded: chain A residue 2357 VAL Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain C residue 427 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 64 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 211 optimal weight: 3.9990 chunk 6 optimal weight: 40.0000 chunk 155 optimal weight: 7.9990 chunk 137 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 233 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.181515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.144490 restraints weight = 22521.855| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.91 r_work: 0.3553 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16635 Z= 0.103 Angle : 0.483 10.456 22738 Z= 0.233 Chirality : 0.037 0.351 2807 Planarity : 0.004 0.043 2823 Dihedral : 8.471 100.696 2473 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.14 % Favored : 96.81 % Rotamer: Outliers : 1.22 % Allowed : 13.27 % Favored : 85.51 % 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: 1.95 (0.20), residues: 2008 helix: 2.61 (0.15), residues: 1299 sheet: -0.24 (0.59), residues: 81 loop : -1.49 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3629 TYR 0.020 0.001 TYR A 998 PHE 0.013 0.001 PHE A1142 TRP 0.013 0.001 TRP A1629 HIS 0.004 0.001 HIS A2352 Details of bonding type rmsd covalent geometry : bond 0.00235 (16634) covalent geometry : angle 0.48317 (22738) hydrogen bonds : bond 0.03563 ( 1071) hydrogen bonds : angle 3.25392 ( 3141) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 2326 MET cc_start: 0.8701 (mmp) cc_final: 0.8327 (mmp) REVERT: A 2345 MET cc_start: 0.8517 (mmt) cc_final: 0.8236 (mmt) outliers start: 18 outliers final: 14 residues processed: 172 average time/residue: 0.1098 time to fit residues: 30.2152 Evaluate side-chains 160 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1512 CYS Chi-restraints excluded: chain A residue 1565 ILE Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1836 TYR Chi-restraints excluded: chain A residue 2357 VAL Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 427 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 86 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 188 optimal weight: 0.3980 chunk 174 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.179033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.142263 restraints weight = 22489.769| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.16 r_work: 0.3504 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 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 0.050 16635 Z= 0.139 Angle : 0.531 12.084 22738 Z= 0.257 Chirality : 0.038 0.365 2807 Planarity : 0.004 0.044 2823 Dihedral : 8.397 99.381 2473 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.78 % Favored : 96.17 % Rotamer: Outliers : 1.56 % Allowed : 14.29 % Favored : 84.16 % 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: 1.82 (0.20), residues: 2008 helix: 2.48 (0.15), residues: 1315 sheet: -0.30 (0.59), residues: 81 loop : -1.56 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3629 TYR 0.022 0.001 TYR A 998 PHE 0.013 0.001 PHE C 310 TRP 0.017 0.001 TRP A3657 HIS 0.004 0.001 HIS A 650 Details of bonding type rmsd covalent geometry : bond 0.00337 (16634) covalent geometry : angle 0.53150 (22738) hydrogen bonds : bond 0.04310 ( 1071) hydrogen bonds : angle 3.34660 ( 3141) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 1352 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8205 (tt) REVERT: A 2345 MET cc_start: 0.8591 (mmt) cc_final: 0.8258 (mmt) outliers start: 23 outliers final: 17 residues processed: 166 average time/residue: 0.1047 time to fit residues: 27.9233 Evaluate side-chains 166 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1512 CYS Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1598 ASP Chi-restraints excluded: chain A residue 1634 VAL Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1836 TYR Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain C residue 427 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 139 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 181 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 211 optimal weight: 0.6980 chunk 11 optimal weight: 20.0000 chunk 134 optimal weight: 0.2980 chunk 10 optimal weight: 40.0000 chunk 120 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.181476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.144895 restraints weight = 22470.330| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.13 r_work: 0.3541 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16635 Z= 0.098 Angle : 0.480 11.682 22738 Z= 0.231 Chirality : 0.037 0.357 2807 Planarity : 0.003 0.044 2823 Dihedral : 8.143 95.315 2473 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.09 % Favored : 96.86 % Rotamer: Outliers : 1.49 % Allowed : 15.37 % Favored : 83.14 % 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: 2.03 (0.20), residues: 2008 helix: 2.66 (0.15), residues: 1305 sheet: -0.21 (0.59), residues: 81 loop : -1.46 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2336 TYR 0.019 0.001 TYR A 998 PHE 0.010 0.001 PHE C 310 TRP 0.012 0.001 TRP A1629 HIS 0.004 0.001 HIS A2352 Details of bonding type rmsd covalent geometry : bond 0.00218 (16634) covalent geometry : angle 0.48038 (22738) hydrogen bonds : bond 0.03405 ( 1071) hydrogen bonds : angle 3.19330 ( 3141) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 1352 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8187 (tt) REVERT: A 2089 ILE cc_start: 0.7930 (mm) cc_final: 0.7594 (mm) REVERT: A 2326 MET cc_start: 0.8685 (mmp) cc_final: 0.8378 (mmp) REVERT: A 2345 MET cc_start: 0.8540 (mmt) cc_final: 0.8214 (mmt) outliers start: 22 outliers final: 18 residues processed: 172 average time/residue: 0.1021 time to fit residues: 28.3466 Evaluate side-chains 171 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1352 LEU Chi-restraints excluded: chain A residue 1512 CYS Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1758 ASN Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1836 TYR Chi-restraints excluded: chain A residue 2357 VAL Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 427 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 136 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 177 optimal weight: 0.0000 chunk 113 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 180 optimal weight: 0.5980 chunk 184 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.182453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.145585 restraints weight = 22398.512| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.98 r_work: 0.3569 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16635 Z= 0.092 Angle : 0.473 10.463 22738 Z= 0.226 Chirality : 0.037 0.374 2807 Planarity : 0.003 0.046 2823 Dihedral : 7.883 91.037 2473 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.29 % Favored : 96.66 % Rotamer: Outliers : 1.56 % Allowed : 15.64 % Favored : 82.80 % 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: 2.17 (0.20), residues: 2008 helix: 2.76 (0.15), residues: 1304 sheet: -0.11 (0.59), residues: 81 loop : -1.40 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3629 TYR 0.019 0.001 TYR A 998 PHE 0.010 0.001 PHE C 310 TRP 0.011 0.001 TRP A2221 HIS 0.004 0.000 HIS A2352 Details of bonding type rmsd covalent geometry : bond 0.00201 (16634) covalent geometry : angle 0.47270 (22738) hydrogen bonds : bond 0.03138 ( 1071) hydrogen bonds : angle 3.10552 ( 3141) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.508 Fit side-chains REVERT: A 2089 ILE cc_start: 0.7925 (mm) cc_final: 0.7589 (mm) REVERT: A 2326 MET cc_start: 0.8619 (mmp) cc_final: 0.8320 (mmp) REVERT: A 2345 MET cc_start: 0.8479 (mmt) cc_final: 0.8226 (mmt) outliers start: 23 outliers final: 16 residues processed: 173 average time/residue: 0.1049 time to fit residues: 29.2650 Evaluate side-chains 163 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1512 CYS Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1758 ASN Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1836 TYR Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 427 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 170 optimal weight: 0.2980 chunk 145 optimal weight: 0.7980 chunk 211 optimal weight: 0.0060 chunk 15 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 209 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 3 optimal weight: 40.0000 chunk 135 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.182463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.145476 restraints weight = 22566.888| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.28 r_work: 0.3556 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16635 Z= 0.096 Angle : 0.493 12.169 22738 Z= 0.236 Chirality : 0.037 0.391 2807 Planarity : 0.003 0.045 2823 Dihedral : 7.705 88.987 2473 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.09 % Favored : 96.86 % Rotamer: Outliers : 1.42 % Allowed : 16.45 % Favored : 82.13 % 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: 2.17 (0.20), residues: 2008 helix: 2.74 (0.15), residues: 1305 sheet: -0.09 (0.59), residues: 81 loop : -1.34 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3629 TYR 0.019 0.001 TYR A 998 PHE 0.014 0.001 PHE C 325 TRP 0.011 0.001 TRP A2221 HIS 0.006 0.001 HIS A1499 Details of bonding type rmsd covalent geometry : bond 0.00212 (16634) covalent geometry : angle 0.49271 (22738) hydrogen bonds : bond 0.03213 ( 1071) hydrogen bonds : angle 3.15068 ( 3141) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.545 Fit side-chains REVERT: A 725 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7659 (pm20) REVERT: A 1563 LYS cc_start: 0.7336 (ptpt) cc_final: 0.7037 (ptpt) REVERT: A 2089 ILE cc_start: 0.7928 (mm) cc_final: 0.7587 (mm) REVERT: A 2326 MET cc_start: 0.8627 (mmp) cc_final: 0.8320 (mmp) REVERT: A 2345 MET cc_start: 0.8490 (mmt) cc_final: 0.8242 (mmt) outliers start: 21 outliers final: 17 residues processed: 167 average time/residue: 0.1117 time to fit residues: 29.6573 Evaluate side-chains 169 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 725 GLN Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1512 CYS Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1598 ASP Chi-restraints excluded: chain A residue 1758 ASN Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1836 TYR Chi-restraints excluded: chain A residue 2357 VAL Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 427 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 108 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 55 optimal weight: 0.1980 chunk 64 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 29 optimal weight: 0.0030 chunk 48 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.182978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.145979 restraints weight = 22599.549| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.16 r_work: 0.3574 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16635 Z= 0.094 Angle : 0.499 13.441 22738 Z= 0.240 Chirality : 0.037 0.405 2807 Planarity : 0.003 0.046 2823 Dihedral : 7.416 85.225 2473 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.04 % Favored : 96.91 % Rotamer: Outliers : 1.35 % Allowed : 16.72 % Favored : 81.92 % 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: 2.19 (0.20), residues: 2008 helix: 2.75 (0.15), residues: 1303 sheet: -0.04 (0.59), residues: 81 loop : -1.32 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3629 TYR 0.019 0.001 TYR A 998 PHE 0.011 0.001 PHE C 325 TRP 0.022 0.001 TRP A2098 HIS 0.004 0.000 HIS A2352 Details of bonding type rmsd covalent geometry : bond 0.00204 (16634) covalent geometry : angle 0.49947 (22738) hydrogen bonds : bond 0.03106 ( 1071) hydrogen bonds : angle 3.14368 ( 3141) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.584 Fit side-chains REVERT: A 725 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7655 (pm20) REVERT: A 1563 LYS cc_start: 0.7327 (ptpt) cc_final: 0.7053 (ptpt) REVERT: A 1607 LEU cc_start: 0.8679 (tp) cc_final: 0.8465 (tp) REVERT: A 2089 ILE cc_start: 0.7922 (mm) cc_final: 0.7583 (mm) REVERT: A 2326 MET cc_start: 0.8600 (mmp) cc_final: 0.8296 (mmp) REVERT: A 2345 MET cc_start: 0.8477 (mmt) cc_final: 0.8235 (mmt) REVERT: C 303 GLN cc_start: 0.7415 (mt0) cc_final: 0.7157 (tt0) REVERT: C 338 GLU cc_start: 0.6543 (mm-30) cc_final: 0.5752 (tt0) outliers start: 20 outliers final: 17 residues processed: 164 average time/residue: 0.1104 time to fit residues: 29.0380 Evaluate side-chains 166 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 602 PHE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 725 GLN Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1512 CYS Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1758 ASN Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1836 TYR Chi-restraints excluded: chain A residue 2357 VAL Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 427 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 121 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 145 optimal weight: 0.0170 chunk 218 optimal weight: 4.9990 chunk 138 optimal weight: 0.1980 chunk 6 optimal weight: 40.0000 chunk 207 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 overall best weight: 1.4424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.179093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.141694 restraints weight = 22518.733| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.42 r_work: 0.3502 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16635 Z= 0.140 Angle : 0.547 12.312 22738 Z= 0.266 Chirality : 0.039 0.413 2807 Planarity : 0.004 0.044 2823 Dihedral : 7.562 87.572 2473 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.97 % Rotamer: Outliers : 1.42 % Allowed : 16.99 % Favored : 81.58 % 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: 1.95 (0.20), residues: 2008 helix: 2.54 (0.15), residues: 1312 sheet: -0.12 (0.59), residues: 81 loop : -1.41 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 903 TYR 0.021 0.001 TYR A 998 PHE 0.011 0.001 PHE A 760 TRP 0.017 0.001 TRP A2098 HIS 0.004 0.001 HIS A 650 Details of bonding type rmsd covalent geometry : bond 0.00338 (16634) covalent geometry : angle 0.54717 (22738) hydrogen bonds : bond 0.04270 ( 1071) hydrogen bonds : angle 3.33925 ( 3141) Misc. bond : bond 0.00014 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.701 Fit side-chains REVERT: A 725 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7733 (pm20) REVERT: A 2089 ILE cc_start: 0.7947 (mm) cc_final: 0.7612 (mm) REVERT: A 2345 MET cc_start: 0.8568 (mmt) cc_final: 0.8261 (mmt) outliers start: 21 outliers final: 17 residues processed: 171 average time/residue: 0.1104 time to fit residues: 30.0729 Evaluate side-chains 175 residues out of total 1843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 725 GLN Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 1047 THR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1512 CYS Chi-restraints excluded: chain A residue 1592 ILE Chi-restraints excluded: chain A residue 1598 ASP Chi-restraints excluded: chain A residue 1758 ASN Chi-restraints excluded: chain A residue 1803 LEU Chi-restraints excluded: chain A residue 1836 TYR Chi-restraints excluded: chain A residue 2357 VAL Chi-restraints excluded: chain A residue 2367 VAL Chi-restraints excluded: chain C residue 390 MET Chi-restraints excluded: chain C residue 427 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 194 optimal weight: 0.7980 chunk 20 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 30.0000 chunk 86 optimal weight: 2.9990 chunk 129 optimal weight: 30.0000 chunk 147 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.180803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.144121 restraints weight = 22484.340| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.13 r_work: 0.3539 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16635 Z= 0.108 Angle : 0.514 13.577 22738 Z= 0.249 Chirality : 0.038 0.406 2807 Planarity : 0.003 0.044 2823 Dihedral : 7.456 85.739 2473 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.54 % Favored : 96.41 % Rotamer: Outliers : 1.49 % Allowed : 16.86 % Favored : 81.65 % 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: 2.03 (0.20), residues: 2008 helix: 2.61 (0.14), residues: 1311 sheet: -0.17 (0.60), residues: 79 loop : -1.37 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3629 TYR 0.020 0.001 TYR A 998 PHE 0.010 0.001 PHE C 310 TRP 0.016 0.001 TRP A2098 HIS 0.004 0.001 HIS A2352 Details of bonding type rmsd covalent geometry : bond 0.00247 (16634) covalent geometry : angle 0.51431 (22738) hydrogen bonds : bond 0.03610 ( 1071) hydrogen bonds : angle 3.25753 ( 3141) Misc. bond : bond 0.00001 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4878.45 seconds wall clock time: 83 minutes 44.96 seconds (5024.96 seconds total)