Starting phenix.real_space_refine on Sun Mar 17 15:45:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orj_13039/03_2024/7orj_13039_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orj_13039/03_2024/7orj_13039.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orj_13039/03_2024/7orj_13039_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orj_13039/03_2024/7orj_13039_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orj_13039/03_2024/7orj_13039_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orj_13039/03_2024/7orj_13039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orj_13039/03_2024/7orj_13039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orj_13039/03_2024/7orj_13039_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7orj_13039/03_2024/7orj_13039_updated.pdb" } resolution = 3.9 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 41 5.49 5 S 110 5.16 5 C 11475 2.51 5 N 3043 2.21 5 O 3527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 100": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A GLU 931": "OE1" <-> "OE2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "A GLU 1087": "OE1" <-> "OE2" Residue "A GLU 1089": "OE1" <-> "OE2" Residue "A GLU 1201": "OE1" <-> "OE2" Residue "A GLU 1270": "OE1" <-> "OE2" Residue "A GLU 1324": "OE1" <-> "OE2" Residue "A GLU 1483": "OE1" <-> "OE2" Residue "A GLU 1509": "OE1" <-> "OE2" Residue "A GLU 1766": "OE1" <-> "OE2" Residue "A GLU 1843": "OE1" <-> "OE2" Residue "A GLU 1945": "OE1" <-> "OE2" Residue "A GLU 1953": "OE1" <-> "OE2" Residue "A GLU 2006": "OE1" <-> "OE2" Residue "A GLU 2035": "OE1" <-> "OE2" Residue "A ASP 2165": "OD1" <-> "OD2" 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: 18197 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 17369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2129, 17369 Classifications: {'peptide': 2129} Link IDs: {'PTRANS': 71, 'TRANS': 2057} Chain breaks: 8 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: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 357 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 5, 'rna3p_pyr': 6} Link IDs: {'rna2p': 5, 'rna3p': 11} 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16054 SG CYS A2064 60.445 21.986 41.983 1.00 82.98 S Time building chain proxies: 9.68, per 1000 atoms: 0.53 Number of scatterers: 18197 At special positions: 0 Unit cell: (114.5, 130.53, 151.14, 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) Zn 1 29.99 S 110 16.00 P 41 15.00 O 3527 8.00 N 3043 7.00 C 11475 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: 7.67 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" SG CYS A2064 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A2169 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A2182 " 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 89 helices and 12 sheets defined 50.2% alpha, 8.5% beta 8 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 11.35 Creating SS restraints... Processing helix chain 'A' and resid 3 through 14 Processing helix chain 'A' and resid 19 through 45 Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 99 through 119 removed outlier: 4.606A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 4.684A 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 199 through 203 removed outlier: 3.584A pdb=" N TRP A 202 " --> pdb=" O PRO A 199 " (cutoff:3.500A) 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 262 removed outlier: 3.630A pdb=" N ASN A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE A 262 " --> pdb=" O SER A 258 " (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 Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'A' and resid 448 through 465 Processing helix chain 'A' and resid 476 through 488 removed outlier: 6.640A pdb=" N SER A 483 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 6.051A 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 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 660 removed outlier: 3.997A pdb=" N LEU A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Proline residue: A 651 - end of helix removed outlier: 4.540A 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: 4.544A pdb=" N TYR A 698 " --> pdb=" O CYS A 694 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASP A 699 " --> pdb=" O PHE A 695 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLN A 702 " --> pdb=" O TYR A 698 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ARG A 703 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 751 Proline residue: A 748 - end of helix removed outlier: 4.044A pdb=" N PHE A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 780 removed outlier: 4.454A pdb=" N VAL A 764 " --> pdb=" O HIS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 813 removed outlier: 3.627A pdb=" N SER A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 3.810A 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 897 through 899 No H-bonds generated for 'chain 'A' and resid 897 through 899' Processing helix chain 'A' and resid 911 through 920 Processing helix chain 'A' and resid 929 through 939 removed outlier: 4.039A pdb=" N ILE A 938 " --> pdb=" O MET A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 979 Processing helix chain 'A' and resid 995 through 1031 removed outlier: 4.114A pdb=" N LEU A1001 " --> pdb=" O LEU A 998 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR A1015 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR A1016 " --> pdb=" O VAL A1013 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG A1021 " --> pdb=" O GLN A1018 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLU A1022 " --> pdb=" O LYS A1019 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP A1024 " --> pdb=" O ARG A1021 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A1029 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1047 Processing helix chain 'A' and resid 1070 through 1078 Processing helix chain 'A' and resid 1085 through 1100 Processing helix chain 'A' and resid 1107 through 1115 Processing helix chain 'A' and resid 1124 through 1129 Processing helix chain 'A' and resid 1149 through 1174 removed outlier: 3.608A 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: 3.663A pdb=" N LEU A1257 " --> pdb=" O ARG A1254 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A1261 " --> pdb=" O THR A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1284 Processing helix chain 'A' and resid 1289 through 1306 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: 3.735A pdb=" N GLU A1380 " --> pdb=" O ASN A1376 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A1381 " --> pdb=" O GLN A1377 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS A1382 " --> pdb=" O ILE A1378 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASN A1383 " --> pdb=" O ALA A1379 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1403 Processing helix chain 'A' and resid 1435 through 1440 removed outlier: 3.914A pdb=" N LYS A1440 " --> pdb=" O GLY A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1451 removed outlier: 3.553A 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 1472 removed outlier: 3.638A pdb=" N VAL A1472 " --> pdb=" O GLU A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1490 removed outlier: 4.232A 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: 3.965A pdb=" N GLN A1510 " --> pdb=" O LEU A1506 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE A1511 " --> pdb=" O PHE A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1549 through 1562 Processing helix chain 'A' and resid 1567 through 1577 Processing helix chain 'A' and resid 1582 through 1593 Processing helix chain 'A' and resid 1623 through 1632 Processing helix chain 'A' and resid 1642 through 1658 removed outlier: 3.859A pdb=" N ARG A1647 " --> pdb=" O THR A1643 " (cutoff:3.500A) Processing helix chain 'A' and resid 1662 through 1676 Processing helix chain 'A' and resid 1681 through 1702 removed outlier: 3.655A pdb=" N THR A1702 " --> pdb=" O TYR A1698 " (cutoff:3.500A) Processing helix chain 'A' and resid 1718 through 1729 Processing helix chain 'A' and resid 1760 through 1778 removed outlier: 3.864A pdb=" N HIS A1773 " --> pdb=" O LYS A1769 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1794 removed outlier: 4.681A pdb=" N SER A1785 " --> pdb=" O SER A1781 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA A1786 " --> pdb=" O LEU A1782 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1811 Processing helix chain 'A' and resid 1813 through 1825 removed outlier: 4.484A pdb=" N THR A1816 " --> pdb=" O TYR A1813 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A1819 " --> pdb=" O THR A1816 " (cutoff:3.500A) Proline residue: A1820 - end of helix removed outlier: 3.643A pdb=" N THR A1825 " --> pdb=" O LEU A1822 " (cutoff:3.500A) Processing helix chain 'A' and resid 1830 through 1840 removed outlier: 4.468A pdb=" N LYS A1840 " --> pdb=" O TYR A1836 " (cutoff:3.500A) Processing helix chain 'A' and resid 1893 through 1904 Processing helix chain 'A' and resid 1944 through 1954 Processing helix chain 'A' and resid 1984 through 1992 removed outlier: 4.045A pdb=" N ASP A1988 " --> pdb=" O ILE A1984 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TYR A1989 " --> pdb=" O ARG A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 2015 through 2020 removed outlier: 4.192A pdb=" N VAL A2019 " --> pdb=" O SER A2016 " (cutoff:3.500A) Processing helix chain 'A' and resid 2033 through 2038 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 Processing helix chain 'A' and resid 2071 through 2076 removed outlier: 3.507A pdb=" N GLU A2075 " --> pdb=" O ASN A2071 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE A2076 " --> pdb=" O ASP A2072 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2071 through 2076' Processing helix chain 'A' and resid 2110 through 2128 removed outlier: 4.107A pdb=" N LYS A2123 " --> pdb=" O GLU A2119 " (cutoff:3.500A) Processing helix chain 'A' and resid 2139 through 2154 removed outlier: 3.678A pdb=" N CYS A2144 " --> pdb=" O GLU A2140 " (cutoff:3.500A) Processing helix chain 'A' and resid 2162 through 2174 Processing helix chain 'A' and resid 2178 through 2180 No H-bonds generated for 'chain 'A' and resid 2178 through 2180' Processing helix chain 'A' and resid 2201 through 2210 Processing helix chain 'A' and resid 2218 through 2236 removed outlier: 3.760A pdb=" N VAL A2221 " --> pdb=" O PRO A2218 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A2222 " --> pdb=" O TRP A2219 " (cutoff:3.500A) removed outlier: 3.584A 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: 7.766A pdb=" N ILE A 90 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU A 125 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ASP A 92 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A 127 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LYS A 94 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.005A 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: 3.664A pdb=" N TRP A 395 " --> pdb=" O GLN A 398 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N MET A 400 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 6.150A 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: 3.902A 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 removed outlier: 3.600A pdb=" N THR A 909 " --> pdb=" O CYS A 843 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 959 through 963 removed outlier: 6.519A pdb=" N GLU A1102 " --> pdb=" O PHE A 945 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N PHE A 947 " --> pdb=" O GLU A1102 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE A1104 " --> pdb=" O PHE A 947 " (cutoff:3.500A) removed outlier: 10.647A pdb=" N ASN A 949 " --> pdb=" O ILE A1104 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS A1101 " --> pdb=" O ILE A1139 " (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 1235 through 1238 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: 3.812A pdb=" N ARG A1870 " --> pdb=" O GLY A1867 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A1883 " --> pdb=" O ILE A1875 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLU A1877 " --> pdb=" O LEU A1881 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU A1881 " --> pdb=" O GLU A1877 " (cutoff:3.500A) removed outlier: 13.071A pdb=" N LYS A1880 " --> pdb=" O THR A1966 " (cutoff:3.500A) removed outlier: 10.405A pdb=" N VAL A1968 " --> pdb=" O LYS A1880 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR A1882 " --> pdb=" O VAL A1968 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL A1970 " --> pdb=" O THR A1882 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A1966 " --> pdb=" O TYR A1929 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE A1927 " --> pdb=" O VAL A1968 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL A1970 " --> pdb=" O TYR A1925 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N TYR A1925 " --> pdb=" O VAL A1970 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS A1942 " --> pdb=" O TYR A1926 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 2084 through 2090 removed outlier: 3.506A pdb=" N GLU A2086 " --> pdb=" O TYR A2100 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE A2096 " --> pdb=" O ILE A2090 " (cutoff:3.500A) 773 hydrogen bonds defined for protein. 2097 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 8.69 Time building geometry restraints manager: 8.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4065 1.33 - 1.45: 4058 1.45 - 1.57: 10259 1.57 - 1.69: 78 1.69 - 1.81: 182 Bond restraints: 18642 Sorted by residual: bond pdb=" C2E GTG P 1 " pdb=" C3E GTG P 1 " ideal model delta sigma weight residual 1.254 1.466 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C5B GTG P 1 " pdb=" C6B GTG P 1 " ideal model delta sigma weight residual 1.538 1.329 0.209 2.00e-02 2.50e+03 1.09e+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=" C3D GTG P 1 " pdb=" C4D GTG P 1 " ideal model delta sigma weight residual 1.298 1.491 -0.193 2.00e-02 2.50e+03 9.32e+01 bond pdb=" C4B GTG P 1 " pdb=" N3B GTG P 1 " ideal model delta sigma weight residual 1.499 1.338 0.161 2.00e-02 2.50e+03 6.49e+01 ... (remaining 18637 not shown) Histogram of bond angle deviations from ideal: 94.69 - 102.59: 154 102.59 - 110.48: 4828 110.48 - 118.38: 9837 118.38 - 126.28: 10199 126.28 - 134.18: 314 Bond angle restraints: 25332 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 93.21 124.33 -31.12 3.00e+00 1.11e-01 1.08e+02 angle pdb=" C1D GTG P 1 " pdb=" N9A GTG P 1 " pdb=" C8A GTG P 1 " ideal model delta sigma weight residual 157.61 127.11 30.50 3.00e+00 1.11e-01 1.03e+02 angle pdb=" C1E GTG P 1 " pdb=" N9B GTG P 1 " pdb=" C4B GTG P 1 " ideal model delta sigma weight residual 152.69 123.51 29.18 3.00e+00 1.11e-01 9.46e+01 angle pdb=" C1E GTG P 1 " pdb=" N9B GTG P 1 " pdb=" C8B GTG P 1 " ideal model delta sigma weight residual 99.21 128.11 -28.90 3.00e+00 1.11e-01 9.28e+01 angle pdb=" PB ATP A2302 " pdb=" O3B ATP A2302 " pdb=" PG ATP A2302 " ideal model delta sigma weight residual 139.87 132.10 7.77 1.00e+00 1.00e+00 6.04e+01 ... (remaining 25327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 10238 18.00 - 36.00: 901 36.00 - 53.99: 175 53.99 - 71.99: 61 71.99 - 89.99: 20 Dihedral angle restraints: 11395 sinusoidal: 5075 harmonic: 6320 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 -56.50 -71.50 1 1.70e+01 3.46e-03 2.27e+01 dihedral pdb=" CA PHE A2084 " pdb=" C PHE A2084 " pdb=" N THR A2085 " pdb=" CA THR A2085 " ideal model delta harmonic sigma weight residual 180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA MET A1128 " pdb=" C MET A1128 " pdb=" N THR A1129 " pdb=" CA THR A1129 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 11392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2581 0.077 - 0.153: 244 0.153 - 0.230: 15 0.230 - 0.306: 8 0.306 - 0.383: 2 Chirality restraints: 2850 Sorted by residual: 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 -2.81 0.38 2.00e-01 2.50e+01 3.67e+00 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 -2.74 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" C2E GTG P 1 " pdb=" C1E GTG P 1 " pdb=" C3E GTG P 1 " pdb=" O2E GTG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.69 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 2847 not shown) Planarity restraints: 3066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A1877 " -0.013 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C GLU A1877 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU A1877 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP A1878 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A2061 " -0.011 2.00e-02 2.50e+03 2.31e-02 5.33e+00 pdb=" C LEU A2061 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU A2061 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE A2062 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A1967 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.75e+00 pdb=" C PRO A1967 " -0.033 2.00e-02 2.50e+03 pdb=" O PRO A1967 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL A1968 " 0.011 2.00e-02 2.50e+03 ... (remaining 3063 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1683 2.74 - 3.28: 18673 3.28 - 3.82: 31482 3.82 - 4.36: 37830 4.36 - 4.90: 63592 Nonbonded interactions: 153260 Sorted by model distance: nonbonded pdb=" OD1 ASP A2178 " pdb="ZN ZN A2301 " model vdw 2.203 2.230 nonbonded pdb=" OG SER A1443 " pdb=" OH TYR A1489 " model vdw 2.206 2.440 nonbonded pdb=" OH TYR A 504 " pdb=" OD1 ASN A 632 " model vdw 2.237 2.440 nonbonded pdb=" O THR A 790 " pdb=" OG1 THR A 793 " model vdw 2.278 2.440 nonbonded pdb=" O ILE A2056 " pdb=" OG SER A2059 " model vdw 2.307 2.440 ... (remaining 153255 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 group one per residue 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: 0.750 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: 0.020 Extract box with map and model: 4.480 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 60.670 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 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 : 0.006 0.212 18642 Z= 0.381 Angle : 0.799 31.116 25332 Z= 0.453 Chirality : 0.047 0.383 2850 Planarity : 0.004 0.051 3066 Dihedral : 14.648 89.989 7291 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.71 % Allowed : 0.81 % Favored : 98.47 % 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: 0.20 (0.18), residues: 2111 helix: 1.28 (0.16), residues: 1085 sheet: 0.23 (0.40), residues: 176 loop : -1.43 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1143 HIS 0.004 0.001 HIS A1185 PHE 0.019 0.002 PHE A1220 TYR 0.015 0.001 TYR A1230 ARG 0.011 0.000 ARG A1668 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 238 time to evaluate : 2.152 Fit side-chains revert: symmetry clash REVERT: A 457 MET cc_start: 0.7939 (tmm) cc_final: 0.7608 (ttp) REVERT: A 625 LEU cc_start: 0.8818 (mt) cc_final: 0.8478 (mt) REVERT: A 995 ASP cc_start: 0.7859 (m-30) cc_final: 0.7610 (m-30) REVERT: A 1025 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7760 (tm-30) REVERT: A 1473 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7663 (p) REVERT: A 1649 LEU cc_start: 0.8886 (mt) cc_final: 0.8675 (mt) outliers start: 14 outliers final: 2 residues processed: 249 average time/residue: 0.2848 time to fit residues: 111.4460 Evaluate side-chains 171 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 168 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 1473 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 0.0770 chunk 124 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 overall best weight: 0.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 332 GLN A 417 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 819 ASN A1233 ASN A1334 ASN A1743 GLN ** A2054 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18642 Z= 0.168 Angle : 0.508 9.023 25332 Z= 0.265 Chirality : 0.040 0.165 2850 Planarity : 0.004 0.051 3066 Dihedral : 11.277 74.602 2894 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.66 % Allowed : 7.18 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.23 (0.18), residues: 2111 helix: 1.28 (0.16), residues: 1089 sheet: 0.29 (0.40), residues: 183 loop : -1.41 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A2201 HIS 0.009 0.001 HIS A 299 PHE 0.032 0.001 PHE A 751 TYR 0.012 0.001 TYR A1230 ARG 0.006 0.000 ARG A1614 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 198 time to evaluate : 2.178 Fit side-chains revert: symmetry clash REVERT: A 457 MET cc_start: 0.7976 (tmm) cc_final: 0.7665 (ttp) REVERT: A 497 HIS cc_start: 0.8283 (OUTLIER) cc_final: 0.7963 (m90) REVERT: A 1055 MET cc_start: 0.7631 (ttp) cc_final: 0.7277 (ttp) REVERT: A 1056 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8015 (pm20) REVERT: A 1309 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6487 (mtt) REVERT: A 1334 ASN cc_start: 0.7515 (m110) cc_final: 0.7047 (m-40) REVERT: A 1649 LEU cc_start: 0.8889 (mt) cc_final: 0.8656 (mt) REVERT: A 1654 GLU cc_start: 0.6679 (tm-30) cc_final: 0.6434 (tp30) REVERT: A 2203 MET cc_start: 0.4120 (OUTLIER) cc_final: 0.3389 (ttp) outliers start: 13 outliers final: 4 residues processed: 204 average time/residue: 0.2735 time to fit residues: 89.4042 Evaluate side-chains 172 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 164 time to evaluate : 2.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain A residue 1767 CYS Chi-restraints excluded: chain A residue 2203 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 210 optimal weight: 0.0570 chunk 173 optimal weight: 7.9990 chunk 193 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 overall best weight: 1.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 932 GLN A1181 ASN A1567 ASN A1571 GLN A1739 HIS ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2049 ASN A2134 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18642 Z= 0.229 Angle : 0.514 8.146 25332 Z= 0.269 Chirality : 0.041 0.180 2850 Planarity : 0.004 0.034 3066 Dihedral : 11.098 74.623 2893 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.22 % Allowed : 9.83 % Favored : 88.95 % 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: 0.23 (0.18), residues: 2111 helix: 1.26 (0.16), residues: 1087 sheet: 0.36 (0.40), residues: 179 loop : -1.38 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2201 HIS 0.004 0.001 HIS A 306 PHE 0.029 0.002 PHE A2084 TYR 0.015 0.001 TYR A1269 ARG 0.003 0.000 ARG A1930 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 177 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 MET cc_start: 0.8043 (tmm) cc_final: 0.7637 (ttp) REVERT: A 497 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.8018 (m90) REVERT: A 1056 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8135 (pm20) REVERT: A 1144 LEU cc_start: 0.8186 (mt) cc_final: 0.7841 (mt) REVERT: A 1309 MET cc_start: 0.7611 (mtt) cc_final: 0.6898 (mtt) REVERT: A 1334 ASN cc_start: 0.7631 (m110) cc_final: 0.7163 (m110) REVERT: A 1610 MET cc_start: 0.7716 (tmm) cc_final: 0.7310 (tmm) REVERT: A 1654 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6425 (tp30) REVERT: A 2228 LYS cc_start: 0.8476 (mmtt) cc_final: 0.7402 (ttmt) outliers start: 24 outliers final: 18 residues processed: 192 average time/residue: 0.2692 time to fit residues: 83.7322 Evaluate side-chains 182 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1024 ASP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1688 MET Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1767 CYS Chi-restraints excluded: chain A residue 1892 THR Chi-restraints excluded: chain A residue 1914 ASN Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2162 THR Chi-restraints excluded: chain A residue 2199 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 0.3980 chunk 146 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 130 optimal weight: 0.0970 chunk 195 optimal weight: 6.9990 chunk 206 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 185 optimal weight: 4.9990 chunk 55 optimal weight: 0.2980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN A1567 ASN ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2134 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18642 Z= 0.131 Angle : 0.459 9.457 25332 Z= 0.241 Chirality : 0.039 0.163 2850 Planarity : 0.003 0.030 3066 Dihedral : 10.938 74.572 2893 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.37 % Allowed : 11.10 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.18), residues: 2111 helix: 1.39 (0.16), residues: 1083 sheet: 0.34 (0.40), residues: 185 loop : -1.30 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1143 HIS 0.003 0.001 HIS A1591 PHE 0.023 0.001 PHE A 751 TYR 0.013 0.001 TYR A1269 ARG 0.004 0.000 ARG A1930 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 180 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 HIS cc_start: 0.8321 (OUTLIER) cc_final: 0.8081 (m90) REVERT: A 1056 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8204 (pm20) REVERT: A 1144 LEU cc_start: 0.8209 (mt) cc_final: 0.7870 (mt) REVERT: A 1309 MET cc_start: 0.7415 (mtt) cc_final: 0.6639 (mtt) REVERT: A 1334 ASN cc_start: 0.7266 (m110) cc_final: 0.7034 (m110) REVERT: A 1610 MET cc_start: 0.7714 (tmm) cc_final: 0.7164 (tmm) REVERT: A 1654 GLU cc_start: 0.6823 (tm-30) cc_final: 0.6381 (tp30) REVERT: A 2228 LYS cc_start: 0.8419 (mmtt) cc_final: 0.7409 (ttmt) outliers start: 27 outliers final: 14 residues processed: 200 average time/residue: 0.2670 time to fit residues: 87.5846 Evaluate side-chains 175 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 159 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1024 ASP Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 2114 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 176 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN A1567 ASN ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 18642 Z= 0.301 Angle : 0.548 9.841 25332 Z= 0.284 Chirality : 0.042 0.179 2850 Planarity : 0.004 0.034 3066 Dihedral : 10.971 74.936 2893 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.58 % Allowed : 12.17 % Favored : 86.25 % 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: 0.20 (0.18), residues: 2111 helix: 1.27 (0.16), residues: 1084 sheet: 0.16 (0.40), residues: 180 loop : -1.40 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A2201 HIS 0.006 0.001 HIS A 306 PHE 0.022 0.002 PHE A 751 TYR 0.015 0.002 TYR A1269 ARG 0.004 0.000 ARG A1930 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 HIS cc_start: 0.8327 (OUTLIER) cc_final: 0.8105 (m90) REVERT: A 655 MET cc_start: 0.7588 (ttm) cc_final: 0.7292 (ttm) REVERT: A 1056 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8134 (pm20) REVERT: A 1334 ASN cc_start: 0.7619 (m110) cc_final: 0.7202 (m110) REVERT: A 1610 MET cc_start: 0.7792 (tmm) cc_final: 0.7141 (tmm) REVERT: A 1654 GLU cc_start: 0.6973 (tm-30) cc_final: 0.6527 (tp30) REVERT: A 1725 MET cc_start: 0.7994 (ttp) cc_final: 0.7542 (ttp) REVERT: A 2228 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7315 (ttmt) outliers start: 31 outliers final: 24 residues processed: 184 average time/residue: 0.2680 time to fit residues: 80.3786 Evaluate side-chains 177 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 497 HIS Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1024 ASP Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain A residue 1547 VAL Chi-restraints excluded: chain A residue 1688 MET Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1846 THR Chi-restraints excluded: chain A residue 1892 THR Chi-restraints excluded: chain A residue 1914 ASN Chi-restraints excluded: chain A residue 2002 VAL Chi-restraints excluded: chain A residue 2058 PHE Chi-restraints excluded: chain A residue 2162 THR Chi-restraints excluded: chain A residue 2199 ILE Chi-restraints excluded: chain A residue 2221 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 4.9990 chunk 186 optimal weight: 0.3980 chunk 40 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18642 Z= 0.163 Angle : 0.481 10.781 25332 Z= 0.249 Chirality : 0.040 0.239 2850 Planarity : 0.003 0.034 3066 Dihedral : 10.903 74.652 2893 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.32 % Allowed : 13.19 % Favored : 85.49 % 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: 0.33 (0.18), residues: 2111 helix: 1.38 (0.16), residues: 1076 sheet: 0.30 (0.40), residues: 181 loop : -1.34 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1143 HIS 0.003 0.001 HIS A1591 PHE 0.022 0.001 PHE A 751 TYR 0.012 0.001 TYR A1989 ARG 0.003 0.000 ARG A1930 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 174 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 569 GLU cc_start: 0.5889 (pp20) cc_final: 0.5637 (pp20) REVERT: A 655 MET cc_start: 0.7506 (ttm) cc_final: 0.7223 (ttm) REVERT: A 1056 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8226 (pm20) REVERT: A 1100 ASP cc_start: 0.6807 (t0) cc_final: 0.6335 (t0) REVERT: A 1334 ASN cc_start: 0.7389 (m110) cc_final: 0.7184 (m110) REVERT: A 1605 MET cc_start: 0.8661 (mmm) cc_final: 0.8288 (mmm) REVERT: A 1610 MET cc_start: 0.7863 (tmm) cc_final: 0.7217 (tmm) REVERT: A 1654 GLU cc_start: 0.6935 (tm-30) cc_final: 0.6521 (tp30) REVERT: A 2228 LYS cc_start: 0.8280 (mmtt) cc_final: 0.7265 (ttmt) outliers start: 26 outliers final: 19 residues processed: 197 average time/residue: 0.2611 time to fit residues: 83.5243 Evaluate side-chains 182 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1024 ASP Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1338 ASP Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1729 LEU Chi-restraints excluded: chain A residue 1846 THR Chi-restraints excluded: chain A residue 1892 THR Chi-restraints excluded: chain A residue 2221 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 151 optimal weight: 0.0170 chunk 174 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 125 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 127 optimal weight: 0.0870 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 HIS ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 18642 Z= 0.150 Angle : 0.474 12.677 25332 Z= 0.245 Chirality : 0.039 0.179 2850 Planarity : 0.003 0.032 3066 Dihedral : 10.776 74.596 2891 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.48 % Allowed : 13.34 % Favored : 85.18 % 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: 0.37 (0.18), residues: 2111 helix: 1.41 (0.16), residues: 1078 sheet: 0.41 (0.41), residues: 181 loop : -1.35 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1143 HIS 0.005 0.001 HIS A2182 PHE 0.043 0.001 PHE A2184 TYR 0.014 0.001 TYR A1269 ARG 0.003 0.000 ARG A1930 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 172 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 569 GLU cc_start: 0.5978 (pp20) cc_final: 0.5743 (pp20) REVERT: A 1014 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7365 (mp0) REVERT: A 1056 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8239 (pm20) REVERT: A 1100 ASP cc_start: 0.6789 (t0) cc_final: 0.6326 (t0) REVERT: A 1654 GLU cc_start: 0.6890 (tm-30) cc_final: 0.6410 (tp30) REVERT: A 1930 ARG cc_start: 0.6280 (mpt90) cc_final: 0.5614 (ttm110) REVERT: A 2228 LYS cc_start: 0.8199 (mmtt) cc_final: 0.7188 (ttmt) outliers start: 29 outliers final: 22 residues processed: 194 average time/residue: 0.2973 time to fit residues: 92.4282 Evaluate side-chains 186 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 163 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1729 LEU Chi-restraints excluded: chain A residue 1839 MET Chi-restraints excluded: chain A residue 1846 THR Chi-restraints excluded: chain A residue 1892 THR Chi-restraints excluded: chain A residue 1938 VAL Chi-restraints excluded: chain A residue 2055 LEU Chi-restraints excluded: chain A residue 2058 PHE Chi-restraints excluded: chain A residue 2221 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 0.4980 chunk 123 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 162 optimal weight: 7.9990 chunk 187 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 18642 Z= 0.159 Angle : 0.485 12.740 25332 Z= 0.250 Chirality : 0.040 0.175 2850 Planarity : 0.003 0.032 3066 Dihedral : 10.752 74.595 2891 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.58 % Allowed : 13.70 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.18), residues: 2111 helix: 1.44 (0.16), residues: 1078 sheet: 0.41 (0.41), residues: 181 loop : -1.29 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1143 HIS 0.002 0.001 HIS A1591 PHE 0.026 0.001 PHE A 751 TYR 0.014 0.001 TYR A1269 ARG 0.006 0.000 ARG A1829 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 165 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 569 GLU cc_start: 0.6085 (pp20) cc_final: 0.5876 (pp20) REVERT: A 1014 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7382 (mp0) REVERT: A 1056 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8221 (pm20) REVERT: A 1100 ASP cc_start: 0.6718 (t0) cc_final: 0.6403 (t0) REVERT: A 1605 MET cc_start: 0.8659 (mmm) cc_final: 0.8334 (mmm) REVERT: A 1654 GLU cc_start: 0.6914 (tm-30) cc_final: 0.6453 (tp30) REVERT: A 1930 ARG cc_start: 0.6280 (mpt90) cc_final: 0.5620 (ttm110) REVERT: A 2184 PHE cc_start: 0.4371 (m-10) cc_final: 0.4037 (m-80) REVERT: A 2228 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7222 (ttmt) outliers start: 31 outliers final: 26 residues processed: 191 average time/residue: 0.2763 time to fit residues: 84.9071 Evaluate side-chains 189 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1024 ASP Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain A residue 1406 ASP Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1729 LEU Chi-restraints excluded: chain A residue 1839 MET Chi-restraints excluded: chain A residue 1846 THR Chi-restraints excluded: chain A residue 1892 THR Chi-restraints excluded: chain A residue 1914 ASN Chi-restraints excluded: chain A residue 1938 VAL Chi-restraints excluded: chain A residue 2055 LEU Chi-restraints excluded: chain A residue 2221 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 7.9990 chunk 180 optimal weight: 0.9980 chunk 192 optimal weight: 0.4980 chunk 115 optimal weight: 6.9990 chunk 83 optimal weight: 0.0000 chunk 150 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 173 optimal weight: 8.9990 chunk 181 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18642 Z= 0.154 Angle : 0.481 13.249 25332 Z= 0.247 Chirality : 0.040 0.163 2850 Planarity : 0.003 0.032 3066 Dihedral : 10.716 74.580 2891 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.48 % Allowed : 13.65 % Favored : 84.88 % 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: 0.44 (0.18), residues: 2111 helix: 1.46 (0.16), residues: 1078 sheet: 0.35 (0.40), residues: 186 loop : -1.29 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1143 HIS 0.002 0.001 HIS A1591 PHE 0.025 0.001 PHE A 751 TYR 0.013 0.001 TYR A1269 ARG 0.006 0.000 ARG A1829 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 177 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7793 (m-40) cc_final: 0.6467 (t0) REVERT: A 569 GLU cc_start: 0.6036 (pp20) cc_final: 0.5796 (pp20) REVERT: A 1056 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8192 (pm20) REVERT: A 1334 ASN cc_start: 0.7206 (m110) cc_final: 0.6976 (m-40) REVERT: A 1605 MET cc_start: 0.8625 (mmm) cc_final: 0.8154 (mmm) REVERT: A 1654 GLU cc_start: 0.6827 (tm-30) cc_final: 0.6515 (tp30) REVERT: A 1858 MET cc_start: 0.6209 (mtt) cc_final: 0.5855 (mtp) REVERT: A 1930 ARG cc_start: 0.6315 (mpt90) cc_final: 0.5608 (ttm110) REVERT: A 2018 MET cc_start: 0.8372 (tmm) cc_final: 0.8142 (tpt) outliers start: 29 outliers final: 25 residues processed: 199 average time/residue: 0.2845 time to fit residues: 90.0976 Evaluate side-chains 194 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 168 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1024 ASP Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain A residue 1406 ASP Chi-restraints excluded: chain A residue 1645 MET Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1729 LEU Chi-restraints excluded: chain A residue 1839 MET Chi-restraints excluded: chain A residue 1846 THR Chi-restraints excluded: chain A residue 1892 THR Chi-restraints excluded: chain A residue 1914 ASN Chi-restraints excluded: chain A residue 1938 VAL Chi-restraints excluded: chain A residue 2055 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 0.2980 chunk 124 optimal weight: 0.0570 chunk 96 optimal weight: 0.1980 chunk 141 optimal weight: 0.7980 chunk 213 optimal weight: 9.9990 chunk 196 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1726 GLN ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18642 Z= 0.128 Angle : 0.478 13.328 25332 Z= 0.245 Chirality : 0.039 0.188 2850 Planarity : 0.003 0.032 3066 Dihedral : 10.676 74.562 2891 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.12 % Allowed : 14.05 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2111 helix: 1.54 (0.16), residues: 1073 sheet: 0.55 (0.41), residues: 181 loop : -1.25 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1143 HIS 0.003 0.000 HIS A1591 PHE 0.024 0.001 PHE A 751 TYR 0.012 0.001 TYR A1269 ARG 0.006 0.000 ARG A1829 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 183 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7817 (m-40) cc_final: 0.6536 (t0) REVERT: A 569 GLU cc_start: 0.5972 (pp20) cc_final: 0.5756 (pp20) REVERT: A 1100 ASP cc_start: 0.6490 (t0) cc_final: 0.6199 (t0) REVERT: A 1605 MET cc_start: 0.8391 (mmm) cc_final: 0.7921 (mmm) REVERT: A 1654 GLU cc_start: 0.6858 (tm-30) cc_final: 0.6534 (tp30) REVERT: A 1858 MET cc_start: 0.6138 (mtt) cc_final: 0.5801 (mtp) REVERT: A 1930 ARG cc_start: 0.6194 (mpt90) cc_final: 0.5595 (ttm110) REVERT: A 2018 MET cc_start: 0.8379 (tmm) cc_final: 0.8130 (tpt) REVERT: A 2228 LYS cc_start: 0.8323 (mmtt) cc_final: 0.7270 (ttmt) outliers start: 22 outliers final: 17 residues processed: 199 average time/residue: 0.2849 time to fit residues: 90.0055 Evaluate side-chains 192 residues out of total 1964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 175 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain A residue 989 MET Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1250 SER Chi-restraints excluded: chain A residue 1331 ILE Chi-restraints excluded: chain A residue 1406 ASP Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1729 LEU Chi-restraints excluded: chain A residue 1839 MET Chi-restraints excluded: chain A residue 1846 THR Chi-restraints excluded: chain A residue 1892 THR Chi-restraints excluded: chain A residue 1914 ASN Chi-restraints excluded: chain A residue 2055 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 174 optimal weight: 0.1980 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1726 GLN ** A1743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.107417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.090222 restraints weight = 47657.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.091925 restraints weight = 27782.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.093123 restraints weight = 18896.573| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18642 Z= 0.146 Angle : 0.481 13.503 25332 Z= 0.246 Chirality : 0.039 0.188 2850 Planarity : 0.003 0.033 3066 Dihedral : 10.656 74.576 2891 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.22 % Allowed : 14.21 % Favored : 84.57 % 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: 0.56 (0.18), residues: 2111 helix: 1.53 (0.16), residues: 1078 sheet: 0.55 (0.41), residues: 181 loop : -1.21 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1143 HIS 0.003 0.001 HIS A1591 PHE 0.025 0.001 PHE A 751 TYR 0.014 0.001 TYR A1269 ARG 0.006 0.000 ARG A1829 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3086.52 seconds wall clock time: 57 minutes 39.77 seconds (3459.77 seconds total)