Starting phenix.real_space_refine on Sun Mar 17 19:32:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ork_13040/03_2024/7ork_13040_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ork_13040/03_2024/7ork_13040.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ork_13040/03_2024/7ork_13040_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ork_13040/03_2024/7ork_13040_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ork_13040/03_2024/7ork_13040_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ork_13040/03_2024/7ork_13040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ork_13040/03_2024/7ork_13040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ork_13040/03_2024/7ork_13040_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ork_13040/03_2024/7ork_13040_updated.pdb" } resolution = 3.1 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= 0.001 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 42 5.49 5 Mg 2 5.21 5 S 116 5.16 5 C 11752 2.51 5 N 3126 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 24": "OD1" <-> "OD2" Residue "A TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 362": "OE1" <-> "OE2" Residue "A TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 597": "OD1" <-> "OD2" Residue "A ASP 621": "OD1" <-> "OD2" Residue "A ASP 668": "OD1" <-> "OD2" Residue "A PHE 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 935": "OD1" <-> "OD2" Residue "A GLU 1025": "OE1" <-> "OE2" Residue "A GLU 1028": "OE1" <-> "OE2" Residue "A GLU 1056": "OE1" <-> "OE2" Residue "A ASP 1115": "OD1" <-> "OD2" Residue "A ASP 1203": "OD1" <-> "OD2" Residue "A ASP 1207": "OD1" <-> "OD2" Residue "A GLU 1237": "OE1" <-> "OE2" Residue "A GLU 1350": "OE1" <-> "OE2" Residue "A GLU 1469": "OE1" <-> "OE2" Residue "A GLU 1612": "OE1" <-> "OE2" Residue "A GLU 1662": "OE1" <-> "OE2" Residue "A PHE 1774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1776": "OD1" <-> "OD2" Residue "A TYR 1868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2032": "OD1" <-> "OD2" Residue "A GLU 2075": "OE1" <-> "OE2" Residue "A GLU 2126": "OE1" <-> "OE2" Residue "A PHE 2129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2131": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18699 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 17799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2182, 17799 Classifications: {'peptide': 2182} Link IDs: {'PTRANS': 72, 'TRANS': 2109} Chain breaks: 6 Chain: "H" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 365 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 14} Chain: "T" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 379 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 6, 'rna3p_pyr': 6} Link IDs: {'rna2p': 5, 'rna3p': 12} Chain: "P" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'GTG': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p_pur': 1} Link IDs: {None: 1} Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 75 Unusual residues: {' MG': 2, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 4, 'water': 41} Link IDs: {None: 44} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16484 SG CYS A2064 49.063 99.939 50.681 1.00118.87 S Time building chain proxies: 10.66, per 1000 atoms: 0.57 Number of scatterers: 18699 At special positions: 0 Unit cell: (113.52, 119.325, 148.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 116 16.00 P 42 15.00 Mg 2 11.99 O 3660 8.00 N 3126 7.00 C 11752 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 - 3.50 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.64 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2303 " pdb="ZN ZN A2303 " - pdb=" NE2 HIS A2169 " pdb="ZN ZN A2303 " - pdb=" NE2 HIS A2182 " pdb="ZN ZN A2303 " - pdb=" SG CYS A2064 " 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4204 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 97 helices and 12 sheets defined 49.5% alpha, 8.3% beta 8 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 12.64 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'A' and resid 20 through 45 Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 99 through 120 removed outlier: 4.024A pdb=" N ILE A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ILE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 159 through 171 Processing helix chain 'A' and resid 176 through 182 Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 216 through 226 Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 248 through 263 removed outlier: 3.631A pdb=" N ASN A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N PHE A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 291 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 320 through 332 Processing helix chain 'A' and resid 341 through 351 Processing helix chain 'A' and resid 357 through 370 removed outlier: 3.646A pdb=" N LYS A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 416 Processing helix chain 'A' and resid 448 through 465 Processing helix chain 'A' and resid 476 through 488 removed outlier: 6.742A pdb=" N SER A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ARG A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 501 Processing helix chain 'A' and resid 503 through 521 removed outlier: 3.592A pdb=" N VAL A 521 " --> pdb=" O ASN A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 619 Proline residue: A 608 - end of helix Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 643 through 659 removed outlier: 4.052A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Proline residue: A 651 - end of helix removed outlier: 4.533A pdb=" N TYR A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 672 Processing helix chain 'A' and resid 681 through 703 removed outlier: 4.633A pdb=" N TYR A 698 " --> pdb=" O CYS A 694 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASP A 699 " --> pdb=" O PHE A 695 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN A 702 " --> pdb=" O TYR A 698 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ARG A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 750 Proline residue: A 748 - end of helix Processing helix chain 'A' and resid 759 through 780 removed outlier: 4.210A pdb=" N VAL A 764 " --> pdb=" O HIS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 813 removed outlier: 3.676A pdb=" N ARG A 813 " --> pdb=" O ALA A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 824 Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 850 through 853 No H-bonds generated for 'chain 'A' and resid 850 through 853' Processing helix chain 'A' and resid 876 through 878 No H-bonds generated for 'chain 'A' and resid 876 through 878' Processing helix chain 'A' and resid 881 through 883 No H-bonds generated for 'chain 'A' and resid 881 through 883' Processing helix chain 'A' and resid 893 through 899 Processing helix chain 'A' and resid 911 through 920 Processing helix chain 'A' and resid 929 through 939 removed outlier: 3.901A pdb=" N ILE A 938 " --> pdb=" O MET A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 979 removed outlier: 3.547A pdb=" N VAL A 974 " --> pdb=" O CYS A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1029 removed outlier: 4.094A pdb=" N LEU A1001 " --> pdb=" O LEU A 998 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A1014 " --> pdb=" O PHE A1011 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR A1015 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR A1016 " --> pdb=" O VAL A1013 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A1017 " --> pdb=" O GLU A1014 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG A1021 " --> pdb=" O GLN A1018 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLU A1022 " --> pdb=" O LYS A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1048 removed outlier: 3.626A pdb=" N GLY A1048 " --> pdb=" O LYS A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1078 Processing helix chain 'A' and resid 1085 through 1100 removed outlier: 3.682A pdb=" N ASP A1100 " --> pdb=" O CYS A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1114 Processing helix chain 'A' and resid 1124 through 1128 Processing helix chain 'A' and resid 1149 through 1174 removed outlier: 3.595A pdb=" N LEU A1174 " --> pdb=" O ALA A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1219 Processing helix chain 'A' and resid 1252 through 1261 removed outlier: 4.315A pdb=" N LEU A1257 " --> pdb=" O ARG A1254 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR A1258 " --> pdb=" O PHE A1255 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY A1261 " --> pdb=" O THR A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1285 Processing helix chain 'A' and resid 1289 through 1306 Processing helix chain 'A' and resid 1318 through 1320 No H-bonds generated for 'chain 'A' and resid 1318 through 1320' Processing helix chain 'A' and resid 1326 through 1328 No H-bonds generated for 'chain 'A' and resid 1326 through 1328' Processing helix chain 'A' and resid 1331 through 1333 No H-bonds generated for 'chain 'A' and resid 1331 through 1333' Processing helix chain 'A' and resid 1341 through 1346 Processing helix chain 'A' and resid 1351 through 1363 Processing helix chain 'A' and resid 1367 through 1369 No H-bonds generated for 'chain 'A' and resid 1367 through 1369' Processing helix chain 'A' and resid 1374 through 1383 removed outlier: 3.646A pdb=" N GLU A1380 " --> pdb=" O ASN A1376 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A1381 " --> pdb=" O GLN A1377 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS A1382 " --> pdb=" O ILE A1378 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ASN A1383 " --> pdb=" O ALA A1379 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1402 Processing helix chain 'A' and resid 1435 through 1439 Processing helix chain 'A' and resid 1442 through 1451 removed outlier: 3.572A pdb=" N LYS A1446 " --> pdb=" O TYR A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1456 through 1466 Processing helix chain 'A' and resid 1468 through 1471 Processing helix chain 'A' and resid 1478 through 1490 removed outlier: 4.274A pdb=" N ASN A1490 " --> pdb=" O ILE A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1497 No H-bonds generated for 'chain 'A' and resid 1494 through 1497' Processing helix chain 'A' and resid 1503 through 1512 removed outlier: 3.637A pdb=" N GLN A1510 " --> pdb=" O LEU A1506 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A1511 " --> pdb=" O PHE A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1549 through 1561 Processing helix chain 'A' and resid 1567 through 1577 Processing helix chain 'A' and resid 1582 through 1593 Processing helix chain 'A' and resid 1613 through 1616 Processing helix chain 'A' and resid 1623 through 1632 Processing helix chain 'A' and resid 1642 through 1658 removed outlier: 3.791A pdb=" N ARG A1647 " --> pdb=" O THR A1643 " (cutoff:3.500A) Processing helix chain 'A' and resid 1661 through 1676 Processing helix chain 'A' and resid 1681 through 1702 removed outlier: 3.568A pdb=" N THR A1702 " --> pdb=" O TYR A1698 " (cutoff:3.500A) Processing helix chain 'A' and resid 1718 through 1729 removed outlier: 3.697A pdb=" N LEU A1729 " --> pdb=" O MET A1725 " (cutoff:3.500A) Processing helix chain 'A' and resid 1757 through 1778 removed outlier: 3.671A pdb=" N HIS A1773 " --> pdb=" O LYS A1769 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1794 removed outlier: 3.548A pdb=" N ARG A1784 " --> pdb=" O SER A1781 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N SER A1785 " --> pdb=" O LEU A1782 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A1786 " --> pdb=" O SER A1783 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A1794 " --> pdb=" O ILE A1791 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1810 Processing helix chain 'A' and resid 1815 through 1817 No H-bonds generated for 'chain 'A' and resid 1815 through 1817' Processing helix chain 'A' and resid 1819 through 1825 Processing helix chain 'A' and resid 1830 through 1837 Processing helix chain 'A' and resid 1839 through 1841 No H-bonds generated for 'chain 'A' and resid 1839 through 1841' Processing helix chain 'A' and resid 1893 through 1904 Processing helix chain 'A' and resid 1944 through 1955 Processing helix chain 'A' and resid 1984 through 1990 removed outlier: 3.957A pdb=" N ASP A1988 " --> pdb=" O ILE A1984 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR A1989 " --> pdb=" O ARG A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 2015 through 2020 removed outlier: 3.977A pdb=" N VAL A2019 " --> pdb=" O SER A2016 " (cutoff:3.500A) Processing helix chain 'A' and resid 2033 through 2037 Processing helix chain 'A' and resid 2040 through 2042 No H-bonds generated for 'chain 'A' and resid 2040 through 2042' Processing helix chain 'A' and resid 2047 through 2051 Processing helix chain 'A' and resid 2055 through 2061 removed outlier: 3.921A pdb=" N LYS A2060 " --> pdb=" O ILE A2056 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU A2061 " --> pdb=" O SER A2057 " (cutoff:3.500A) Processing helix chain 'A' and resid 2073 through 2076 Processing helix chain 'A' and resid 2110 through 2128 removed outlier: 3.696A pdb=" N LYS A2123 " --> pdb=" O GLU A2119 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2154 removed outlier: 3.620A pdb=" N ILE A2152 " --> pdb=" O VAL A2148 " (cutoff:3.500A) Processing helix chain 'A' and resid 2162 through 2174 Processing helix chain 'A' and resid 2179 through 2182 No H-bonds generated for 'chain 'A' and resid 2179 through 2182' Processing helix chain 'A' and resid 2201 through 2209 removed outlier: 4.046A pdb=" N ARG A2205 " --> pdb=" O TRP A2201 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A2206 " --> pdb=" O VAL A2202 " (cutoff:3.500A) Processing helix chain 'A' and resid 2218 through 2236 removed outlier: 3.717A pdb=" N VAL A2221 " --> pdb=" O PRO A2218 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET A2222 " --> pdb=" O TRP A2219 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N THR A2223 " --> pdb=" O ASN A2220 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 80 through 84 removed outlier: 8.478A pdb=" N ILE A 90 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N GLU A 125 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ASP A 92 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL A 127 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LYS A 94 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE A 129 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 293 through 295 Processing sheet with id= C, first strand: chain 'A' and resid 594 through 596 removed outlier: 4.757A pdb=" N VAL A 558 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP A 395 " --> pdb=" O GLN A 398 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET A 400 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL A 393 " --> pdb=" O MET A 400 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 562 through 565 removed outlier: 3.612A pdb=" N GLY A 586 " --> pdb=" O CYS A 583 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 842 through 846 Processing sheet with id= F, first strand: chain 'A' and resid 959 through 962 removed outlier: 6.451A pdb=" N GLU A1102 " --> pdb=" O PHE A 945 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N PHE A 947 " --> pdb=" O GLU A1102 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ILE A1104 " --> pdb=" O PHE A 947 " (cutoff:3.500A) removed outlier: 10.489A pdb=" N ASN A 949 " --> pdb=" O ILE A1104 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1230 through 1232 Processing sheet with id= H, first strand: chain 'A' and resid 1236 through 1238 removed outlier: 3.644A pdb=" N GLU A1247 " --> pdb=" O LEU A1244 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1594 through 1596 Processing sheet with id= J, first strand: chain 'A' and resid 1606 through 1608 Processing sheet with id= K, first strand: chain 'A' and resid 1844 through 1847 removed outlier: 3.784A pdb=" N ARG A1870 " --> pdb=" O GLY A1867 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLU A1877 " --> pdb=" O LEU A1881 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU A1881 " --> pdb=" O GLU A1877 " (cutoff:3.500A) removed outlier: 12.778A pdb=" N LYS A1880 " --> pdb=" O THR A1966 " (cutoff:3.500A) removed outlier: 10.379A pdb=" N VAL A1968 " --> pdb=" O LYS A1880 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR A1882 " --> pdb=" O VAL A1968 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N VAL A1970 " --> pdb=" O THR A1882 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A1927 " --> pdb=" O VAL A1968 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N VAL A1970 " --> pdb=" O TYR A1925 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N TYR A1925 " --> pdb=" O VAL A1970 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 2083 through 2090 removed outlier: 4.323A pdb=" N PHE A2096 " --> pdb=" O ILE A2090 " (cutoff:3.500A) 761 hydrogen bonds defined for protein. 2058 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 9.57 Time building geometry restraints manager: 8.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3457 1.33 - 1.45: 4812 1.45 - 1.57: 10565 1.57 - 1.69: 80 1.69 - 1.81: 192 Bond restraints: 19106 Sorted by residual: bond pdb=" C2E GTG P 1 " pdb=" C3E GTG P 1 " ideal model delta sigma weight residual 1.254 1.492 -0.238 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C3D GTG P 1 " pdb=" C4D GTG P 1 " ideal model delta sigma weight residual 1.298 1.512 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C5B GTG P 1 " pdb=" C6B GTG P 1 " ideal model delta sigma weight residual 1.538 1.330 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C5A GTG P 1 " pdb=" C6A GTG P 1 " ideal model delta sigma weight residual 1.539 1.335 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C4B GTG P 1 " pdb=" N3B GTG P 1 " ideal model delta sigma weight residual 1.499 1.340 0.159 2.00e-02 2.50e+03 6.31e+01 ... (remaining 19101 not shown) Histogram of bond angle deviations from ideal: 95.31 - 104.17: 376 104.17 - 113.03: 10488 113.03 - 121.89: 11381 121.89 - 130.75: 3629 130.75 - 139.61: 86 Bond angle restraints: 25960 Sorted by residual: angle pdb=" C1D GTG P 1 " pdb=" N9A GTG P 1 " pdb=" C4A GTG P 1 " ideal model delta sigma weight residual 93.21 126.93 -33.72 3.00e+00 1.11e-01 1.26e+02 angle pdb=" C1D GTG P 1 " pdb=" N9A GTG P 1 " pdb=" C8A GTG P 1 " ideal model delta sigma weight residual 157.61 124.80 32.81 3.00e+00 1.11e-01 1.20e+02 angle pdb=" C1E GTG P 1 " pdb=" N9B GTG P 1 " pdb=" C4B GTG P 1 " ideal model delta sigma weight residual 152.69 126.62 26.07 3.00e+00 1.11e-01 7.55e+01 angle pdb=" C1E GTG P 1 " pdb=" N9B GTG P 1 " pdb=" C8B GTG P 1 " ideal model delta sigma weight residual 99.21 125.16 -25.95 3.00e+00 1.11e-01 7.48e+01 angle pdb=" C PHE A2131 " pdb=" CA PHE A2131 " pdb=" CB PHE A2131 " ideal model delta sigma weight residual 111.36 101.01 10.35 1.63e+00 3.76e-01 4.03e+01 ... (remaining 25955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10570 17.95 - 35.90: 813 35.90 - 53.85: 211 53.85 - 71.80: 65 71.80 - 89.75: 23 Dihedral angle restraints: 11682 sinusoidal: 5206 harmonic: 6476 Sorted by residual: dihedral pdb=" O4' C T 21 " pdb=" C1' C T 21 " pdb=" N1 C T 21 " pdb=" C2 C T 21 " ideal model delta sinusoidal sigma weight residual -128.00 -57.57 -70.43 1 1.70e+01 3.46e-03 2.21e+01 dihedral pdb=" C PHE A2131 " pdb=" N PHE A2131 " pdb=" CA PHE A2131 " pdb=" CB PHE A2131 " ideal model delta harmonic sigma weight residual -122.60 -111.47 -11.13 0 2.50e+00 1.60e-01 1.98e+01 dihedral pdb=" C THR A2093 " pdb=" N THR A2093 " pdb=" CA THR A2093 " pdb=" CB THR A2093 " ideal model delta harmonic sigma weight residual -122.00 -132.22 10.22 0 2.50e+00 1.60e-01 1.67e+01 ... (remaining 11679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2603 0.078 - 0.156: 274 0.156 - 0.235: 32 0.235 - 0.313: 4 0.313 - 0.391: 3 Chirality restraints: 2916 Sorted by residual: chirality pdb=" C3D GTG P 1 " pdb=" C2D GTG P 1 " pdb=" C4D GTG P 1 " pdb=" O3D GTG P 1 " both_signs ideal model delta sigma weight residual False -2.38 -2.77 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" C3E GTG P 1 " pdb=" C2E GTG P 1 " pdb=" C4E GTG P 1 " pdb=" O3E GTG P 1 " both_signs ideal model delta sigma weight residual False -2.43 -2.78 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA PHE A2131 " pdb=" N PHE A2131 " pdb=" C PHE A2131 " pdb=" CB PHE A2131 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 2913 not shown) Planarity restraints: 3146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A2199 " 0.019 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C ILE A2199 " -0.064 2.00e-02 2.50e+03 pdb=" O ILE A2199 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN A2200 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1892 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO A1893 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A1893 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A1893 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A2130 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.45e+00 pdb=" C THR A2130 " 0.040 2.00e-02 2.50e+03 pdb=" O THR A2130 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE A2131 " -0.014 2.00e-02 2.50e+03 ... (remaining 3143 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 101 2.58 - 3.16: 15244 3.16 - 3.74: 29603 3.74 - 4.32: 43779 4.32 - 4.90: 70796 Nonbonded interactions: 159523 Sorted by model distance: nonbonded pdb=" OD2 ASP A1060 " pdb="MG MG A2302 " model vdw 1.996 2.170 nonbonded pdb=" OD1 ASP A2178 " pdb="ZN ZN A2303 " model vdw 2.074 2.230 nonbonded pdb=" OD2 ASP A1187 " pdb="MG MG A2302 " model vdw 2.145 2.170 nonbonded pdb=" O MET A1061 " pdb="MG MG A2302 " model vdw 2.166 2.170 nonbonded pdb=" OE1 GLN A 301 " pdb=" O HOH A2401 " model vdw 2.245 2.440 ... (remaining 159518 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: 5.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 17.560 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 63.780 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 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 0.238 19106 Z= 0.422 Angle : 0.789 33.724 25960 Z= 0.470 Chirality : 0.051 0.391 2916 Planarity : 0.004 0.067 3146 Dihedral : 14.710 89.753 7478 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.04 % Allowed : 0.94 % Favored : 98.01 % Cbeta Deviations : 0.10 % 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: 0.32 (0.18), residues: 2168 helix: 1.24 (0.16), residues: 1094 sheet: -0.38 (0.37), residues: 199 loop : -0.93 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2160 HIS 0.004 0.001 HIS A1855 PHE 0.031 0.001 PHE A1795 TYR 0.019 0.001 TYR A 677 ARG 0.007 0.000 ARG A1949 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 224 time to evaluate : 1.942 Fit side-chains REVERT: A 10 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8283 (mt) REVERT: A 1963 ASN cc_start: 0.8400 (t0) cc_final: 0.7881 (t0) REVERT: A 2035 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7355 (mm-30) outliers start: 21 outliers final: 4 residues processed: 240 average time/residue: 0.3433 time to fit residues: 122.4966 Evaluate side-chains 196 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 191 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 1988 ASP Chi-restraints excluded: chain A residue 2162 THR Chi-restraints excluded: chain A residue 2163 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 199 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 469 ASN A1202 ASN A1658 ASN A2054 ASN A2134 ASN A2169 HIS A2225 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19106 Z= 0.170 Angle : 0.461 9.029 25960 Z= 0.245 Chirality : 0.039 0.210 2916 Planarity : 0.004 0.060 3146 Dihedral : 11.060 74.775 2966 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.75 % Allowed : 5.17 % Favored : 94.08 % 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: 0.49 (0.18), residues: 2168 helix: 1.35 (0.16), residues: 1099 sheet: -0.10 (0.39), residues: 184 loop : -0.85 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1143 HIS 0.003 0.001 HIS A1855 PHE 0.017 0.001 PHE A1795 TYR 0.015 0.001 TYR A 677 ARG 0.003 0.000 ARG A2106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 196 time to evaluate : 2.074 Fit side-chains REVERT: A 10 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8400 (mt) REVERT: A 597 ASP cc_start: 0.7912 (p0) cc_final: 0.7574 (p0) REVERT: A 599 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: A 2005 ASP cc_start: 0.7695 (OUTLIER) cc_final: 0.7453 (t0) REVERT: A 2035 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7388 (mm-30) outliers start: 15 outliers final: 8 residues processed: 206 average time/residue: 0.3351 time to fit residues: 104.1702 Evaluate side-chains 203 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 192 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2137 ILE Chi-restraints excluded: chain A residue 2162 THR Chi-restraints excluded: chain A residue 2214 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 55 optimal weight: 0.0870 chunk 200 optimal weight: 6.9990 chunk 216 optimal weight: 0.0970 chunk 178 optimal weight: 3.9990 chunk 198 optimal weight: 0.0670 chunk 68 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 469 ASN A 752 ASN A1243 ASN A1634 ASN A1658 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19106 Z= 0.105 Angle : 0.410 7.238 25960 Z= 0.218 Chirality : 0.038 0.178 2916 Planarity : 0.003 0.056 3146 Dihedral : 10.768 81.545 2963 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.90 % Allowed : 6.46 % Favored : 92.64 % 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: 0.70 (0.18), residues: 2168 helix: 1.54 (0.16), residues: 1105 sheet: 0.04 (0.40), residues: 179 loop : -0.80 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1143 HIS 0.006 0.001 HIS A1935 PHE 0.012 0.001 PHE A1395 TYR 0.018 0.001 TYR A 106 ARG 0.006 0.000 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 211 time to evaluate : 2.413 Fit side-chains REVERT: A 10 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8443 (mt) REVERT: A 597 ASP cc_start: 0.7899 (p0) cc_final: 0.7600 (p0) REVERT: A 1115 ASP cc_start: 0.7657 (m-30) cc_final: 0.7451 (p0) REVERT: A 2005 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7445 (t0) REVERT: A 2035 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7377 (mm-30) REVERT: A 2229 LYS cc_start: 0.7340 (mmmt) cc_final: 0.7076 (tptm) outliers start: 18 outliers final: 11 residues processed: 223 average time/residue: 0.3255 time to fit residues: 111.1577 Evaluate side-chains 204 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 995 ASP Chi-restraints excluded: chain A residue 1935 HIS Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2054 ASN Chi-restraints excluded: chain A residue 2162 THR Chi-restraints excluded: chain A residue 2211 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 0.6980 chunk 150 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 190 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A1658 ASN A1935 HIS A2225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19106 Z= 0.222 Angle : 0.454 7.687 25960 Z= 0.241 Chirality : 0.040 0.200 2916 Planarity : 0.003 0.054 3146 Dihedral : 10.827 83.308 2963 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.14 % Allowed : 7.61 % Favored : 91.25 % 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: 0.73 (0.18), residues: 2168 helix: 1.51 (0.16), residues: 1107 sheet: 0.14 (0.40), residues: 184 loop : -0.75 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2219 HIS 0.005 0.001 HIS A1935 PHE 0.021 0.001 PHE A1613 TYR 0.016 0.001 TYR A 677 ARG 0.004 0.000 ARG A 595 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 194 time to evaluate : 2.149 Fit side-chains REVERT: A 2005 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7514 (t0) REVERT: A 2035 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7430 (mm-30) outliers start: 23 outliers final: 16 residues processed: 205 average time/residue: 0.3347 time to fit residues: 104.6868 Evaluate side-chains 199 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 182 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1524 ILE Chi-restraints excluded: chain A residue 1873 THR Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2054 ASN Chi-restraints excluded: chain A residue 2162 THR Chi-restraints excluded: chain A residue 2214 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 181 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 190 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A1185 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19106 Z= 0.253 Angle : 0.463 7.737 25960 Z= 0.247 Chirality : 0.040 0.185 2916 Planarity : 0.003 0.055 3146 Dihedral : 10.877 82.888 2963 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.39 % Allowed : 8.40 % Favored : 90.20 % 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: 0.71 (0.18), residues: 2168 helix: 1.46 (0.16), residues: 1108 sheet: 0.19 (0.39), residues: 194 loop : -0.73 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2219 HIS 0.003 0.001 HIS A1954 PHE 0.018 0.001 PHE A1768 TYR 0.016 0.001 TYR A 677 ARG 0.004 0.000 ARG A1949 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 184 time to evaluate : 2.100 Fit side-chains REVERT: A 2005 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7526 (t0) outliers start: 28 outliers final: 20 residues processed: 200 average time/residue: 0.3403 time to fit residues: 103.3191 Evaluate side-chains 202 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 181 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1524 ILE Chi-restraints excluded: chain A residue 1871 SER Chi-restraints excluded: chain A residue 1873 THR Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2054 ASN Chi-restraints excluded: chain A residue 2162 THR Chi-restraints excluded: chain A residue 2214 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 212 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A1634 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19106 Z= 0.187 Angle : 0.437 7.477 25960 Z= 0.232 Chirality : 0.039 0.210 2916 Planarity : 0.003 0.056 3146 Dihedral : 10.799 83.587 2963 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.29 % Allowed : 9.30 % Favored : 89.41 % 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: 0.80 (0.18), residues: 2168 helix: 1.54 (0.16), residues: 1107 sheet: 0.25 (0.40), residues: 189 loop : -0.69 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2219 HIS 0.003 0.001 HIS A1954 PHE 0.017 0.001 PHE A1613 TYR 0.014 0.001 TYR A 106 ARG 0.005 0.000 ARG A1949 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 186 time to evaluate : 1.895 Fit side-chains REVERT: A 2005 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7489 (t0) outliers start: 26 outliers final: 19 residues processed: 203 average time/residue: 0.3288 time to fit residues: 101.1536 Evaluate side-chains 201 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 181 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1524 ILE Chi-restraints excluded: chain A residue 1871 SER Chi-restraints excluded: chain A residue 1873 THR Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2054 ASN Chi-restraints excluded: chain A residue 2162 THR Chi-restraints excluded: chain A residue 2214 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 118 optimal weight: 0.2980 chunk 212 optimal weight: 9.9990 chunk 132 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19106 Z= 0.159 Angle : 0.431 7.321 25960 Z= 0.229 Chirality : 0.039 0.196 2916 Planarity : 0.003 0.056 3146 Dihedral : 10.741 83.808 2963 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.24 % Allowed : 9.70 % Favored : 89.06 % 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: 0.89 (0.18), residues: 2168 helix: 1.63 (0.16), residues: 1101 sheet: 0.32 (0.39), residues: 194 loop : -0.66 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1143 HIS 0.002 0.001 HIS A 565 PHE 0.017 0.001 PHE A1613 TYR 0.014 0.001 TYR A 106 ARG 0.006 0.000 ARG A1949 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 187 time to evaluate : 2.214 Fit side-chains REVERT: A 1115 ASP cc_start: 0.7222 (p0) cc_final: 0.7021 (p0) REVERT: A 2005 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7502 (t0) outliers start: 25 outliers final: 22 residues processed: 202 average time/residue: 0.3318 time to fit residues: 101.5476 Evaluate side-chains 205 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 182 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1524 ILE Chi-restraints excluded: chain A residue 1871 SER Chi-restraints excluded: chain A residue 1873 THR Chi-restraints excluded: chain A residue 1885 GLU Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2054 ASN Chi-restraints excluded: chain A residue 2162 THR Chi-restraints excluded: chain A residue 2214 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19106 Z= 0.184 Angle : 0.440 7.366 25960 Z= 0.234 Chirality : 0.039 0.194 2916 Planarity : 0.003 0.056 3146 Dihedral : 10.742 83.485 2963 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.24 % Allowed : 9.80 % Favored : 88.96 % 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: 0.91 (0.18), residues: 2168 helix: 1.64 (0.16), residues: 1101 sheet: 0.34 (0.39), residues: 194 loop : -0.65 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2219 HIS 0.003 0.001 HIS A 565 PHE 0.029 0.001 PHE A1613 TYR 0.020 0.001 TYR A1883 ARG 0.006 0.000 ARG A1949 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 181 time to evaluate : 2.216 Fit side-chains REVERT: A 878 PHE cc_start: 0.8599 (m-80) cc_final: 0.8355 (m-80) REVERT: A 1115 ASP cc_start: 0.7276 (p0) cc_final: 0.7063 (p0) REVERT: A 2005 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7487 (t0) REVERT: A 2035 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7308 (mm-30) outliers start: 25 outliers final: 21 residues processed: 198 average time/residue: 0.3166 time to fit residues: 95.3961 Evaluate side-chains 202 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 180 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1524 ILE Chi-restraints excluded: chain A residue 1871 SER Chi-restraints excluded: chain A residue 1873 THR Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2005 ASP Chi-restraints excluded: chain A residue 2054 ASN Chi-restraints excluded: chain A residue 2162 THR Chi-restraints excluded: chain A residue 2214 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 chunk 197 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 178 optimal weight: 0.6980 chunk 186 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 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 8 GLN ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 19106 Z= 0.159 Angle : 0.428 7.230 25960 Z= 0.228 Chirality : 0.039 0.191 2916 Planarity : 0.003 0.056 3146 Dihedral : 10.691 83.745 2963 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.24 % Allowed : 10.04 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.98 (0.19), residues: 2168 helix: 1.69 (0.16), residues: 1096 sheet: 0.37 (0.40), residues: 184 loop : -0.59 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2219 HIS 0.002 0.001 HIS A 565 PHE 0.020 0.001 PHE A1613 TYR 0.017 0.001 TYR A1883 ARG 0.007 0.000 ARG A1949 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 189 time to evaluate : 2.357 Fit side-chains REVERT: A 878 PHE cc_start: 0.8593 (m-80) cc_final: 0.8355 (m-80) REVERT: A 1115 ASP cc_start: 0.7322 (p0) cc_final: 0.7121 (p0) REVERT: A 2035 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7321 (mm-30) outliers start: 25 outliers final: 19 residues processed: 205 average time/residue: 0.3405 time to fit residues: 106.3177 Evaluate side-chains 206 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 187 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1524 ILE Chi-restraints excluded: chain A residue 1871 SER Chi-restraints excluded: chain A residue 1873 THR Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2054 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 219 optimal weight: 8.9990 chunk 201 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19106 Z= 0.199 Angle : 0.445 7.347 25960 Z= 0.237 Chirality : 0.039 0.209 2916 Planarity : 0.003 0.056 3146 Dihedral : 10.726 83.292 2962 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.04 % Allowed : 10.44 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.92 (0.18), residues: 2168 helix: 1.64 (0.16), residues: 1102 sheet: 0.36 (0.40), residues: 184 loop : -0.63 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2219 HIS 0.003 0.001 HIS A 565 PHE 0.020 0.001 PHE A1613 TYR 0.018 0.001 TYR A1883 ARG 0.007 0.000 ARG A1949 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4336 Ramachandran restraints generated. 2168 Oldfield, 0 Emsley, 2168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 2.321 Fit side-chains REVERT: A 878 PHE cc_start: 0.8599 (m-80) cc_final: 0.8354 (m-80) REVERT: A 1115 ASP cc_start: 0.7396 (p0) cc_final: 0.7188 (p0) REVERT: A 2035 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7345 (mm-30) outliers start: 21 outliers final: 20 residues processed: 195 average time/residue: 0.3580 time to fit residues: 106.5377 Evaluate side-chains 199 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 179 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 231 TYR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 732 PHE Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1160 MET Chi-restraints excluded: chain A residue 1524 ILE Chi-restraints excluded: chain A residue 1871 SER Chi-restraints excluded: chain A residue 1873 THR Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2054 ASN Chi-restraints excluded: chain A residue 2214 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.0040 chunk 53 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 73 optimal weight: 0.0470 chunk 179 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 overall best weight: 0.9494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.113087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.080030 restraints weight = 27893.749| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.98 r_work: 0.2719 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19106 Z= 0.175 Angle : 0.437 7.276 25960 Z= 0.233 Chirality : 0.039 0.190 2916 Planarity : 0.003 0.056 3146 Dihedral : 10.710 83.382 2962 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.99 % Allowed : 10.59 % Favored : 88.41 % 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: 0.97 (0.19), residues: 2168 helix: 1.67 (0.16), residues: 1098 sheet: 0.37 (0.40), residues: 184 loop : -0.59 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2219 HIS 0.002 0.001 HIS A 565 PHE 0.029 0.001 PHE A1613 TYR 0.018 0.001 TYR A1883 ARG 0.008 0.000 ARG A1949 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4085.64 seconds wall clock time: 75 minutes 1.99 seconds (4501.99 seconds total)