Starting phenix.real_space_refine (version: dev) on Tue Feb 28 00:55:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pgq_13392/02_2023/7pgq_13392_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pgq_13392/02_2023/7pgq_13392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pgq_13392/02_2023/7pgq_13392.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pgq_13392/02_2023/7pgq_13392.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pgq_13392/02_2023/7pgq_13392_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pgq_13392/02_2023/7pgq_13392_trim_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.004 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 31508 Number of models: 1 Model: "" Number of chains: 3 Chain: "F" Number of atoms: 21053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1320, 21053 Classifications: {'peptide': 1320} Link IDs: {'PTRANS': 53, 'TRANS': 1266} Chain breaks: 5 Chain: "N" Number of atoms: 10405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 10405 Classifications: {'peptide': 650} Link IDs: {'PTRANS': 27, 'TRANS': 622} Chain breaks: 1 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {' ZN': 1, 'PEV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6857 SG CYS F1032 32.721 57.243 84.664 1.00118.24 S Time building chain proxies: 14.78, per 1000 atoms: 0.47 Number of scatterers: 31508 At special positions: 0 Unit cell: (135.88, 115.24, 154.8, 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 99 16.00 P 1 15.00 O 2897 8.00 N 2647 7.00 C 10056 6.00 H 15807 1.00 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=0, symmetry=0 Time building additional restraints: 24.43 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F2902 " pdb="ZN ZN F2902 " - pdb=" NE2 HIS F1558 " pdb="ZN ZN F2902 " - pdb=" NE2 HIS F1576 " pdb="ZN ZN F2902 " - pdb=" SG CYS F1032 " 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3788 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 4 sheets defined 62.5% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'F' and resid 484 through 502 removed outlier: 3.505A pdb=" N TYR F 489 " --> pdb=" O GLU F 485 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS F 490 " --> pdb=" O THR F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 532 removed outlier: 4.235A pdb=" N LEU F 532 " --> pdb=" O GLY F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 551 removed outlier: 3.764A pdb=" N GLU F 547 " --> pdb=" O GLN F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 561 removed outlier: 4.267A pdb=" N ASP F 559 " --> pdb=" O LEU F 555 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEU F 560 " --> pdb=" O ASP F 556 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TRP F 561 " --> pdb=" O SER F 557 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 555 through 561' Processing helix chain 'F' and resid 569 through 587 removed outlier: 3.574A pdb=" N GLN F 576 " --> pdb=" O GLU F 572 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS F 584 " --> pdb=" O TYR F 580 " (cutoff:3.500A) Processing helix chain 'F' and resid 593 through 617 removed outlier: 3.696A pdb=" N LEU F 597 " --> pdb=" O SER F 593 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS F 598 " --> pdb=" O THR F 594 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP F 599 " --> pdb=" O GLU F 595 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU F 602 " --> pdb=" O LYS F 598 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 692 removed outlier: 4.018A pdb=" N LYS F 686 " --> pdb=" O GLN F 682 " (cutoff:3.500A) Processing helix chain 'F' and resid 700 through 720 removed outlier: 3.844A pdb=" N PHE F 710 " --> pdb=" O ALA F 706 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ARG F 711 " --> pdb=" O MET F 707 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N HIS F 712 " --> pdb=" O SER F 708 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU F 713 " --> pdb=" O CYS F 709 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU F 716 " --> pdb=" O HIS F 712 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA F 717 " --> pdb=" O LEU F 713 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP F 718 " --> pdb=" O CYS F 714 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE F 719 " --> pdb=" O GLU F 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 724 through 727 No H-bonds generated for 'chain 'F' and resid 724 through 727' Processing helix chain 'F' and resid 735 through 745 removed outlier: 3.505A pdb=" N MET F 739 " --> pdb=" O TYR F 735 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU F 740 " --> pdb=" O ASN F 736 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE F 741 " --> pdb=" O THR F 737 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA F 742 " --> pdb=" O PHE F 738 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER F 743 " --> pdb=" O MET F 739 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 765 removed outlier: 3.854A pdb=" N ARG F 758 " --> pdb=" O ALA F 754 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG F 765 " --> pdb=" O ALA F 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 771 through 793 removed outlier: 4.202A pdb=" N GLU F 778 " --> pdb=" O THR F 774 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS F 783 " --> pdb=" O ASP F 779 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS F 789 " --> pdb=" O GLU F 785 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU F 790 " --> pdb=" O GLN F 786 " (cutoff:3.500A) Processing helix chain 'F' and resid 832 through 846 Processing helix chain 'F' and resid 849 through 851 No H-bonds generated for 'chain 'F' and resid 849 through 851' Processing helix chain 'F' and resid 890 through 901 removed outlier: 3.671A pdb=" N LEU F 901 " --> pdb=" O ARG F 897 " (cutoff:3.500A) Processing helix chain 'F' and resid 910 through 923 removed outlier: 3.785A pdb=" N ASP F 919 " --> pdb=" O THR F 915 " (cutoff:3.500A) Processing helix chain 'F' and resid 930 through 944 removed outlier: 3.924A pdb=" N ASN F 935 " --> pdb=" O PRO F 931 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE F 944 " --> pdb=" O THR F 940 " (cutoff:3.500A) Processing helix chain 'F' and resid 957 through 973 removed outlier: 3.770A pdb=" N ALA F 966 " --> pdb=" O GLU F 962 " (cutoff:3.500A) Processing helix chain 'F' and resid 980 through 983 No H-bonds generated for 'chain 'F' and resid 980 through 983' Processing helix chain 'F' and resid 989 through 1000 Processing helix chain 'F' and resid 1006 through 1023 removed outlier: 3.704A pdb=" N GLN F1010 " --> pdb=" O VAL F1006 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU F1020 " --> pdb=" O CYS F1016 " (cutoff:3.500A) Processing helix chain 'F' and resid 1034 through 1048 removed outlier: 4.132A pdb=" N LYS F1040 " --> pdb=" O LYS F1036 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP F1047 " --> pdb=" O GLU F1043 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TRP F1048 " --> pdb=" O TYR F1044 " (cutoff:3.500A) Processing helix chain 'F' and resid 1053 through 1057 Processing helix chain 'F' and resid 1060 through 1079 removed outlier: 4.231A pdb=" N LEU F1064 " --> pdb=" O VAL F1061 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP F1069 " --> pdb=" O ARG F1066 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET F1073 " --> pdb=" O GLN F1070 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL F1077 " --> pdb=" O GLU F1074 " (cutoff:3.500A) Processing helix chain 'F' and resid 1095 through 1116 removed outlier: 3.513A pdb=" N SER F1100 " --> pdb=" O MET F1096 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR F1106 " --> pdb=" O LEU F1102 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU F1109 " --> pdb=" O LYS F1105 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP F1116 " --> pdb=" O ASN F1112 " (cutoff:3.500A) Processing helix chain 'F' and resid 1135 through 1155 removed outlier: 3.694A pdb=" N MET F1149 " --> pdb=" O THR F1145 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA F1155 " --> pdb=" O ASN F1151 " (cutoff:3.500A) Processing helix chain 'F' and resid 1162 through 1169 removed outlier: 4.624A pdb=" N GLY F1166 " --> pdb=" O HIS F1163 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR F1169 " --> pdb=" O GLY F1166 " (cutoff:3.500A) Processing helix chain 'F' and resid 1173 through 1188 removed outlier: 3.537A pdb=" N ILE F1186 " --> pdb=" O VAL F1182 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU F1187 " --> pdb=" O LEU F1183 " (cutoff:3.500A) Processing helix chain 'F' and resid 1196 through 1204 removed outlier: 4.262A pdb=" N ALA F1202 " --> pdb=" O GLU F1198 " (cutoff:3.500A) Processing helix chain 'F' and resid 1206 through 1212 removed outlier: 4.009A pdb=" N GLU F1210 " --> pdb=" O GLU F1206 " (cutoff:3.500A) Processing helix chain 'F' and resid 1222 through 1230 removed outlier: 3.589A pdb=" N ASN F1229 " --> pdb=" O MET F1225 " (cutoff:3.500A) Processing helix chain 'F' and resid 1233 through 1249 removed outlier: 4.391A pdb=" N ASP F1237 " --> pdb=" O SER F1234 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU F1239 " --> pdb=" O TRP F1236 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL F1244 " --> pdb=" O ARG F1241 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE F1247 " --> pdb=" O VAL F1244 " (cutoff:3.500A) Processing helix chain 'F' and resid 1253 through 1267 removed outlier: 3.605A pdb=" N LYS F1263 " --> pdb=" O ASN F1259 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU F1264 " --> pdb=" O MET F1260 " (cutoff:3.500A) Processing helix chain 'F' and resid 1271 through 1276 removed outlier: 3.563A pdb=" N PHE F1275 " --> pdb=" O MET F1271 " (cutoff:3.500A) Processing helix chain 'F' and resid 1280 through 1310 removed outlier: 3.702A pdb=" N MET F1285 " --> pdb=" O ALA F1281 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA F1294 " --> pdb=" O LYS F1290 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N THR F1295 " --> pdb=" O VAL F1291 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR F1296 " --> pdb=" O TYR F1292 " (cutoff:3.500A) Proline residue: F1303 - end of helix removed outlier: 3.728A pdb=" N ILE F1307 " --> pdb=" O PRO F1303 " (cutoff:3.500A) Processing helix chain 'F' and resid 1332 through 1352 Processing helix chain 'F' and resid 1359 through 1378 Processing helix chain 'F' and resid 1401 through 1412 Processing helix chain 'F' and resid 1414 through 1419 removed outlier: 3.617A pdb=" N ILE F1418 " --> pdb=" O ILE F1414 " (cutoff:3.500A) Processing helix chain 'F' and resid 1421 through 1424 No H-bonds generated for 'chain 'F' and resid 1421 through 1424' Processing helix chain 'F' and resid 1433 through 1451 removed outlier: 3.793A pdb=" N GLY F1438 " --> pdb=" O ARG F1434 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU F1439 " --> pdb=" O ILE F1435 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA F1450 " --> pdb=" O LEU F1446 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN F1451 " --> pdb=" O GLN F1447 " (cutoff:3.500A) Processing helix chain 'F' and resid 1459 through 1483 Proline residue: F1463 - end of helix removed outlier: 4.270A pdb=" N ASP F1466 " --> pdb=" O ARG F1462 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N PHE F1467 " --> pdb=" O PRO F1463 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL F1468 " --> pdb=" O PHE F1464 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS F1469 " --> pdb=" O ASN F1465 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER F1470 " --> pdb=" O ASP F1466 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN F1471 " --> pdb=" O PHE F1467 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASP F1473 " --> pdb=" O LYS F1469 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ALA F1474 " --> pdb=" O SER F1470 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE F1482 " --> pdb=" O PHE F1478 " (cutoff:3.500A) Processing helix chain 'F' and resid 1501 through 1513 removed outlier: 3.777A pdb=" N LEU F1505 " --> pdb=" O ASP F1501 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA F1506 " --> pdb=" O GLY F1502 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN F1513 " --> pdb=" O ARG F1509 " (cutoff:3.500A) Processing helix chain 'F' and resid 1515 through 1524 removed outlier: 3.556A pdb=" N GLY F1519 " --> pdb=" O GLN F1515 " (cutoff:3.500A) Processing helix chain 'F' and resid 1531 through 1533 No H-bonds generated for 'chain 'F' and resid 1531 through 1533' Processing helix chain 'F' and resid 1535 through 1546 Processing helix chain 'F' and resid 1566 through 1575 Processing helix chain 'F' and resid 1578 through 1580 No H-bonds generated for 'chain 'F' and resid 1578 through 1580' Processing helix chain 'F' and resid 1584 through 1590 removed outlier: 3.818A pdb=" N LYS F1588 " --> pdb=" O PHE F1584 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR F1589 " --> pdb=" O LYS F1585 " (cutoff:3.500A) Processing helix chain 'F' and resid 1620 through 1632 removed outlier: 3.605A pdb=" N ILE F1624 " --> pdb=" O GLY F1620 " (cutoff:3.500A) Processing helix chain 'F' and resid 1656 through 1665 removed outlier: 3.856A pdb=" N LYS F1661 " --> pdb=" O ASP F1657 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TRP F1662 " --> pdb=" O PHE F1658 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE F1663 " --> pdb=" O LEU F1659 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL F1664 " --> pdb=" O SER F1660 " (cutoff:3.500A) Processing helix chain 'F' and resid 1671 through 1673 No H-bonds generated for 'chain 'F' and resid 1671 through 1673' Processing helix chain 'F' and resid 1684 through 1692 Processing helix chain 'F' and resid 1694 through 1700 removed outlier: 4.920A pdb=" N GLY F1699 " --> pdb=" O ARG F1695 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU F1700 " --> pdb=" O LEU F1696 " (cutoff:3.500A) Processing helix chain 'F' and resid 1712 through 1718 removed outlier: 4.054A pdb=" N ALA F1716 " --> pdb=" O PRO F1712 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU F1717 " --> pdb=" O GLY F1713 " (cutoff:3.500A) Processing helix chain 'F' and resid 1728 through 1733 Processing helix chain 'F' and resid 1817 through 1834 removed outlier: 3.604A pdb=" N SER F1823 " --> pdb=" O ALA F1819 " (cutoff:3.500A) Processing helix chain 'F' and resid 1847 through 1849 No H-bonds generated for 'chain 'F' and resid 1847 through 1849' Processing helix chain 'F' and resid 1851 through 1863 removed outlier: 3.576A pdb=" N ILE F1857 " --> pdb=" O THR F1853 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY F1863 " --> pdb=" O LEU F1859 " (cutoff:3.500A) Processing helix chain 'F' and resid 1867 through 1881 removed outlier: 3.550A pdb=" N SER F1871 " --> pdb=" O PRO F1867 " (cutoff:3.500A) Processing helix chain 'F' and resid 1911 through 1918 Processing helix chain 'F' and resid 1920 through 1936 removed outlier: 4.214A pdb=" N LEU F1924 " --> pdb=" O HIS F1921 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU F1927 " --> pdb=" O LEU F1924 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU F1928 " --> pdb=" O GLU F1925 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER F1935 " --> pdb=" O SER F1932 " (cutoff:3.500A) Processing helix chain 'F' and resid 1939 through 1952 removed outlier: 3.660A pdb=" N HIS F1943 " --> pdb=" O ILE F1939 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU F1944 " --> pdb=" O GLU F1940 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR F1950 " --> pdb=" O LEU F1946 " (cutoff:3.500A) Proline residue: F1951 - end of helix Processing helix chain 'N' and resid 1959 through 1961 No H-bonds generated for 'chain 'N' and resid 1959 through 1961' Processing helix chain 'N' and resid 1968 through 1984 removed outlier: 3.566A pdb=" N THR N1972 " --> pdb=" O ARG N1968 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA N1973 " --> pdb=" O GLN N1969 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE N1983 " --> pdb=" O ILE N1979 " (cutoff:3.500A) Processing helix chain 'N' and resid 1989 through 2002 removed outlier: 3.934A pdb=" N ALA N1994 " --> pdb=" O PRO N1990 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TRP N1997 " --> pdb=" O GLN N1993 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY N1998 " --> pdb=" O ALA N1994 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN N2002 " --> pdb=" O GLY N1998 " (cutoff:3.500A) Processing helix chain 'N' and resid 2004 through 2021 removed outlier: 4.477A pdb=" N ASP N2008 " --> pdb=" O ASP N2005 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL N2009 " --> pdb=" O LEU N2006 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU N2011 " --> pdb=" O ASP N2008 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR N2020 " --> pdb=" O THR N2017 " (cutoff:3.500A) Processing helix chain 'N' and resid 2026 through 2040 removed outlier: 3.607A pdb=" N ALA N2032 " --> pdb=" O ALA N2028 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP N2033 " --> pdb=" O GLU N2029 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL N2036 " --> pdb=" O ALA N2032 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA N2037 " --> pdb=" O ASP N2033 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER N2040 " --> pdb=" O VAL N2036 " (cutoff:3.500A) Processing helix chain 'N' and resid 2043 through 2060 removed outlier: 4.205A pdb=" N SER N2048 " --> pdb=" O LYS N2044 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY N2052 " --> pdb=" O SER N2048 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG N2053 " --> pdb=" O LYS N2049 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS N2056 " --> pdb=" O GLY N2052 " (cutoff:3.500A) Processing helix chain 'N' and resid 2069 through 2071 No H-bonds generated for 'chain 'N' and resid 2069 through 2071' Processing helix chain 'N' and resid 2073 through 2092 removed outlier: 4.225A pdb=" N ASP N2076 " --> pdb=" O LEU N2073 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE N2080 " --> pdb=" O ASP N2077 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR N2084 " --> pdb=" O LEU N2081 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE N2090 " --> pdb=" O MET N2087 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ASN N2091 " --> pdb=" O LEU N2088 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN N2092 " --> pdb=" O SER N2089 " (cutoff:3.500A) Processing helix chain 'N' and resid 2096 through 2107 Proline residue: N2101 - end of helix removed outlier: 3.651A pdb=" N VAL N2106 " --> pdb=" O TYR N2102 " (cutoff:3.500A) Processing helix chain 'N' and resid 2116 through 2135 removed outlier: 3.607A pdb=" N THR N2122 " --> pdb=" O LEU N2118 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS N2123 " --> pdb=" O ARG N2119 " (cutoff:3.500A) Processing helix chain 'N' and resid 2143 through 2157 removed outlier: 3.862A pdb=" N GLN N2147 " --> pdb=" O GLU N2143 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL N2148 " --> pdb=" O GLU N2144 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER N2157 " --> pdb=" O LEU N2153 " (cutoff:3.500A) Processing helix chain 'N' and resid 2159 through 2165 removed outlier: 3.544A pdb=" N LEU N2163 " --> pdb=" O PRO N2159 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU N2164 " --> pdb=" O LYS N2160 " (cutoff:3.500A) Processing helix chain 'N' and resid 2173 through 2177 Processing helix chain 'N' and resid 2199 through 2217 removed outlier: 3.559A pdb=" N GLU N2203 " --> pdb=" O LEU N2199 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR N2204 " --> pdb=" O THR N2200 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE N2212 " --> pdb=" O ALA N2208 " (cutoff:3.500A) Processing helix chain 'N' and resid 2225 through 2237 removed outlier: 3.699A pdb=" N PHE N2236 " --> pdb=" O LEU N2232 " (cutoff:3.500A) Processing helix chain 'N' and resid 2245 through 2255 removed outlier: 3.599A pdb=" N VAL N2251 " --> pdb=" O ARG N2247 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE N2252 " --> pdb=" O ALA N2248 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS N2254 " --> pdb=" O VAL N2250 " (cutoff:3.500A) Processing helix chain 'N' and resid 2261 through 2280 removed outlier: 3.688A pdb=" N GLN N2266 " --> pdb=" O GLY N2262 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS N2273 " --> pdb=" O ARG N2269 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU N2275 " --> pdb=" O LEU N2271 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU N2279 " --> pdb=" O LEU N2275 " (cutoff:3.500A) Processing helix chain 'N' and resid 2289 through 2304 removed outlier: 3.515A pdb=" N THR N2294 " --> pdb=" O LEU N2290 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS N2300 " --> pdb=" O ILE N2296 " (cutoff:3.500A) Proline residue: N2303 - end of helix Processing helix chain 'N' and resid 2310 through 2325 removed outlier: 4.639A pdb=" N LEU N2315 " --> pdb=" O HIS N2312 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TRP N2317 " --> pdb=" O ALA N2314 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL N2318 " --> pdb=" O LEU N2315 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA N2319 " --> pdb=" O PHE N2316 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN N2324 " --> pdb=" O ALA N2321 " (cutoff:3.500A) Processing helix chain 'N' and resid 2328 through 2347 removed outlier: 3.593A pdb=" N ALA N2336 " --> pdb=" O SER N2332 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU N2337 " --> pdb=" O ALA N2333 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN N2340 " --> pdb=" O ALA N2336 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER N2347 " --> pdb=" O HIS N2343 " (cutoff:3.500A) Processing helix chain 'N' and resid 2356 through 2362 Processing helix chain 'N' and resid 2368 through 2378 removed outlier: 4.003A pdb=" N GLN N2373 " --> pdb=" O TRP N2369 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET N2374 " --> pdb=" O HIS N2370 " (cutoff:3.500A) Processing helix chain 'N' and resid 2386 through 2392 removed outlier: 4.312A pdb=" N VAL N2391 " --> pdb=" O ASN N2387 " (cutoff:3.500A) Processing helix chain 'N' and resid 2396 through 2399 Processing helix chain 'N' and resid 2403 through 2424 removed outlier: 3.884A pdb=" N ALA N2407 " --> pdb=" O PRO N2403 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG N2408 " --> pdb=" O ALA N2404 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN N2421 " --> pdb=" O LEU N2417 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS N2422 " --> pdb=" O THR N2418 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG N2424 " --> pdb=" O VAL N2420 " (cutoff:3.500A) Processing helix chain 'N' and resid 2437 through 2441 Processing helix chain 'N' and resid 2447 through 2452 Processing helix chain 'N' and resid 2613 through 2629 removed outlier: 4.067A pdb=" N LEU N2619 " --> pdb=" O ILE N2615 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU N2620 " --> pdb=" O GLN N2616 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU N2623 " --> pdb=" O LEU N2619 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL N2627 " --> pdb=" O LEU N2623 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR N2629 " --> pdb=" O THR N2625 " (cutoff:3.500A) Processing helix chain 'N' and resid 2633 through 2649 removed outlier: 3.517A pdb=" N TYR N2642 " --> pdb=" O ILE N2638 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU N2645 " --> pdb=" O GLU N2641 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA N2646 " --> pdb=" O TYR N2642 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL N2648 " --> pdb=" O ALA N2644 " (cutoff:3.500A) Processing helix chain 'N' and resid 2654 through 2671 removed outlier: 3.948A pdb=" N HIS N2658 " --> pdb=" O PRO N2655 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ASN N2659 " --> pdb=" O VAL N2656 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU N2660 " --> pdb=" O VAL N2657 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N SER N2663 " --> pdb=" O LEU N2660 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS N2664 " --> pdb=" O LEU N2661 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE N2665 " --> pdb=" O ASP N2662 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN N2666 " --> pdb=" O SER N2663 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU N2669 " --> pdb=" O ASN N2666 " (cutoff:3.500A) Processing helix chain 'N' and resid 2675 through 2691 Proline residue: N2680 - end of helix Processing helix chain 'N' and resid 2700 through 2702 No H-bonds generated for 'chain 'N' and resid 2700 through 2702' Processing helix chain 'N' and resid 2729 through 2742 removed outlier: 3.886A pdb=" N LYS N2733 " --> pdb=" O GLU N2729 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'F' and resid 1605 through 1609 removed outlier: 7.503A pdb=" N GLU F1640 " --> pdb=" O PHE F1606 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N TYR F1608 " --> pdb=" O GLU F1640 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL F1642 " --> pdb=" O TYR F1608 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE F1641 " --> pdb=" O SER F1675 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL F1677 " --> pdb=" O ILE F1641 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL F1643 " --> pdb=" O VAL F1677 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE F1679 " --> pdb=" O VAL F1643 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 1743 through 1745 removed outlier: 3.919A pdb=" N THR F1751 " --> pdb=" O LYS F1745 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'F' and resid 1770 through 1772 Processing sheet with id= D, first strand: chain 'F' and resid 1798 through 1801 removed outlier: 3.646A pdb=" N PHE F1812 " --> pdb=" O PHE F1799 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1791 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.58 Time building geometry restraints manager: 25.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 15765 1.03 - 1.23: 47 1.23 - 1.42: 6534 1.42 - 1.62: 9330 1.62 - 1.81: 155 Bond restraints: 31831 Sorted by residual: bond pdb=" C4 PEV F2901 " pdb=" C5 PEV F2901 " ideal model delta sigma weight residual 1.511 1.547 -0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" C1 PEV F2901 " pdb=" O3P PEV F2901 " ideal model delta sigma weight residual 1.407 1.443 -0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" O4P PEV F2901 " pdb=" P PEV F2901 " ideal model delta sigma weight residual 1.638 1.605 0.033 2.00e-02 2.50e+03 2.78e+00 bond pdb=" C4 PEV F2901 " pdb=" O4P PEV F2901 " ideal model delta sigma weight residual 1.418 1.450 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C2 PEV F2901 " pdb=" O2 PEV F2901 " ideal model delta sigma weight residual 1.432 1.462 -0.030 2.00e-02 2.50e+03 2.29e+00 ... (remaining 31826 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.04: 358 106.04 - 113.04: 38020 113.04 - 120.03: 9257 120.03 - 127.03: 9809 127.03 - 134.03: 192 Bond angle restraints: 57636 Sorted by residual: angle pdb=" O3P PEV F2901 " pdb=" P PEV F2901 " pdb=" O4P PEV F2901 " ideal model delta sigma weight residual 93.57 104.60 -11.03 3.00e+00 1.11e-01 1.35e+01 angle pdb=" N VAL F 551 " pdb=" CA VAL F 551 " pdb=" C VAL F 551 " ideal model delta sigma weight residual 112.35 108.77 3.58 1.41e+00 5.03e-01 6.44e+00 angle pdb=" N PRO F1535 " pdb=" CA PRO F1535 " pdb=" C PRO F1535 " ideal model delta sigma weight residual 112.47 117.25 -4.78 2.06e+00 2.36e-01 5.38e+00 angle pdb=" C GLU F1459 " pdb=" N HIS F1460 " pdb=" CA HIS F1460 " ideal model delta sigma weight residual 120.38 123.50 -3.12 1.37e+00 5.33e-01 5.17e+00 angle pdb=" C2 PEV F2901 " pdb=" C3 PEV F2901 " pdb=" O3 PEV F2901 " ideal model delta sigma weight residual 112.90 107.15 5.75 3.00e+00 1.11e-01 3.67e+00 ... (remaining 57631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 12270 17.62 - 35.24: 477 35.24 - 52.86: 74 52.86 - 70.48: 21 70.48 - 88.10: 6 Dihedral angle restraints: 12848 sinusoidal: 6054 harmonic: 6794 Sorted by residual: dihedral pdb=" CA SER N2093 " pdb=" C SER N2093 " pdb=" N LEU N2094 " pdb=" CA LEU N2094 " ideal model delta harmonic sigma weight residual 180.00 160.54 19.46 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ARG F1534 " pdb=" C ARG F1534 " pdb=" N PRO F1535 " pdb=" CA PRO F1535 " ideal model delta harmonic sigma weight residual -180.00 -161.08 -18.92 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ASN F1856 " pdb=" CB ASN F1856 " pdb=" CG ASN F1856 " pdb=" OD1 ASN F1856 " ideal model delta sinusoidal sigma weight residual 120.00 -165.54 -74.46 2 2.00e+01 2.50e-03 1.11e+01 ... (remaining 12845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2079 0.042 - 0.084: 353 0.084 - 0.126: 89 0.126 - 0.168: 2 0.168 - 0.210: 1 Chirality restraints: 2524 Sorted by residual: chirality pdb=" C2 PEV F2901 " pdb=" C1 PEV F2901 " pdb=" C3 PEV F2901 " pdb=" O2 PEV F2901 " both_signs ideal model delta sigma weight residual False 2.36 2.57 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PRO F1535 " pdb=" N PRO F1535 " pdb=" C PRO F1535 " pdb=" CB PRO F1535 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ILE N2724 " pdb=" N ILE N2724 " pdb=" C ILE N2724 " pdb=" CB ILE N2724 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 ... (remaining 2521 not shown) Planarity restraints: 4621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR N2066 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO N2067 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO N2067 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO N2067 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F1083 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO F1084 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO F1084 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO F1084 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F1866 " -0.016 5.00e-02 4.00e+02 2.44e-02 9.51e-01 pdb=" N PRO F1867 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO F1867 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO F1867 " -0.014 5.00e-02 4.00e+02 ... (remaining 4618 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1082 2.18 - 2.78: 63102 2.78 - 3.39: 82934 3.39 - 3.99: 102320 3.99 - 4.60: 165245 Nonbonded interactions: 414683 Sorted by model distance: nonbonded pdb=" O ALA N2644 " pdb=" HG SER N2647 " model vdw 1.574 1.850 nonbonded pdb=" O SER F1150 " pdb="HD22 ASN F1154 " model vdw 1.583 1.850 nonbonded pdb=" OD2 ASP F1172 " pdb=" H THR F1175 " model vdw 1.585 1.850 nonbonded pdb=" O GLN F 912 " pdb="HD22 ASN F 916 " model vdw 1.593 1.850 nonbonded pdb=" OD1 ASP F1644 " pdb=" HG1 THR F1646 " model vdw 1.601 1.850 ... (remaining 414678 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 Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1 5.49 5 S 99 5.16 5 C 10056 2.51 5 N 2647 2.21 5 O 2897 1.98 5 H 15807 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.380 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: 0.450 Extract box with map and model: 4.520 Check model and map are aligned: 0.420 Process input model: 99.140 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.290 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 : 0.003 0.036 16024 Z= 0.186 Angle : 0.453 11.027 21715 Z= 0.239 Chirality : 0.035 0.210 2524 Planarity : 0.003 0.041 2739 Dihedral : 10.457 88.096 5930 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.91 % 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: -0.24 (0.19), residues: 1954 helix: 0.40 (0.16), residues: 1142 sheet: 0.30 (0.69), residues: 72 loop : -0.98 (0.22), residues: 740 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 197 average time/residue: 0.7350 time to fit residues: 207.1720 Evaluate side-chains 119 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 2.783 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.6383 time to fit residues: 10.0807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 166 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 154 optimal weight: 0.0670 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 overall best weight: 1.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 682 GLN F 697 ASN ** F 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1577 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 16024 Z= 0.231 Angle : 0.569 6.527 21715 Z= 0.315 Chirality : 0.037 0.165 2524 Planarity : 0.004 0.048 2739 Dihedral : 4.682 55.096 2131 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.07 % Favored : 96.88 % Rotamer Outliers : 0.97 % 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: 0.03 (0.19), residues: 1954 helix: 0.60 (0.15), residues: 1171 sheet: 0.33 (0.67), residues: 71 loop : -0.88 (0.23), residues: 712 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 130 average time/residue: 0.6138 time to fit residues: 123.8944 Evaluate side-chains 109 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 2.501 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.5432 time to fit residues: 11.6883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 179 optimal weight: 0.0770 chunk 193 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N2421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 16024 Z= 0.210 Angle : 0.508 6.822 21715 Z= 0.273 Chirality : 0.035 0.145 2524 Planarity : 0.003 0.046 2739 Dihedral : 4.556 54.302 2131 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.81 % Favored : 97.13 % Rotamer Outliers : 0.51 % 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: 0.29 (0.19), residues: 1954 helix: 0.84 (0.15), residues: 1176 sheet: 0.32 (0.67), residues: 65 loop : -0.81 (0.23), residues: 713 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 113 average time/residue: 0.5993 time to fit residues: 106.5728 Evaluate side-chains 98 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 2.642 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.4693 time to fit residues: 5.7525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 177 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 120 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 190 optimal weight: 0.7980 chunk 170 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 16024 Z= 0.143 Angle : 0.471 5.653 21715 Z= 0.246 Chirality : 0.034 0.140 2524 Planarity : 0.003 0.040 2739 Dihedral : 4.380 54.447 2131 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.02 % Favored : 96.93 % Rotamer Outliers : 0.57 % 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: 0.69 (0.19), residues: 1954 helix: 1.22 (0.15), residues: 1183 sheet: 0.22 (0.66), residues: 65 loop : -0.77 (0.23), residues: 706 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 110 average time/residue: 0.5999 time to fit residues: 103.8093 Evaluate side-chains 99 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 3.230 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.3834 time to fit residues: 6.9573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 108 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 131 optimal weight: 0.0980 chunk 0 optimal weight: 30.0000 chunk 97 optimal weight: 8.9990 chunk 170 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 16024 Z= 0.169 Angle : 0.462 6.657 21715 Z= 0.241 Chirality : 0.034 0.136 2524 Planarity : 0.003 0.043 2739 Dihedral : 4.331 54.176 2131 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % Rotamer Outliers : 0.40 % 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: 0.87 (0.19), residues: 1954 helix: 1.39 (0.15), residues: 1179 sheet: 0.12 (0.65), residues: 65 loop : -0.70 (0.23), residues: 710 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 102 average time/residue: 0.6107 time to fit residues: 97.9523 Evaluate side-chains 99 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 2.762 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.4104 time to fit residues: 8.0108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 171 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 16024 Z= 0.164 Angle : 0.458 6.554 21715 Z= 0.238 Chirality : 0.034 0.135 2524 Planarity : 0.003 0.042 2739 Dihedral : 4.287 54.273 2131 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.92 % Favored : 97.03 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.19), residues: 1954 helix: 1.51 (0.15), residues: 1182 sheet: 0.09 (0.65), residues: 65 loop : -0.66 (0.23), residues: 707 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 100 average time/residue: 0.6258 time to fit residues: 98.0069 Evaluate side-chains 93 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 2.572 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.5605 time to fit residues: 4.4107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 21 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 189 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1054 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 16024 Z= 0.373 Angle : 0.560 6.516 21715 Z= 0.300 Chirality : 0.037 0.131 2524 Planarity : 0.003 0.048 2739 Dihedral : 4.636 51.956 2131 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.25 % Favored : 95.70 % Rotamer Outliers : 0.57 % 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: 0.35 (0.19), residues: 1954 helix: 0.95 (0.15), residues: 1178 sheet: -0.02 (0.65), residues: 65 loop : -0.88 (0.23), residues: 711 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 100 average time/residue: 0.6393 time to fit residues: 98.0077 Evaluate side-chains 97 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 2.537 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.5850 time to fit residues: 9.5343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 75 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 120 optimal weight: 0.0010 chunk 129 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 overall best weight: 1.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1826 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 16024 Z= 0.158 Angle : 0.474 7.372 21715 Z= 0.245 Chirality : 0.034 0.138 2524 Planarity : 0.003 0.067 2739 Dihedral : 4.486 53.381 2131 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.53 % Favored : 96.42 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.19), residues: 1954 helix: 1.31 (0.15), residues: 1187 sheet: 0.03 (0.66), residues: 65 loop : -0.76 (0.23), residues: 702 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 95 average time/residue: 0.6494 time to fit residues: 96.2469 Evaluate side-chains 92 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 2.381 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.4551 time to fit residues: 4.8978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 181 optimal weight: 0.3980 chunk 165 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 16024 Z= 0.210 Angle : 0.491 8.204 21715 Z= 0.255 Chirality : 0.035 0.131 2524 Planarity : 0.003 0.053 2739 Dihedral : 4.517 55.906 2131 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.99 % Favored : 95.96 % Rotamer Outliers : 0.34 % 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: 0.77 (0.19), residues: 1954 helix: 1.33 (0.15), residues: 1187 sheet: 0.04 (0.66), residues: 65 loop : -0.82 (0.23), residues: 702 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 95 average time/residue: 0.6250 time to fit residues: 92.7148 Evaluate side-chains 94 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 2.554 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.4543 time to fit residues: 6.2629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 114 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 180 optimal weight: 0.0980 chunk 156 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 120 optimal weight: 0.2980 chunk 95 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 16024 Z= 0.134 Angle : 0.471 9.096 21715 Z= 0.238 Chirality : 0.034 0.138 2524 Planarity : 0.003 0.050 2739 Dihedral : 4.318 51.857 2131 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.12 % Favored : 96.83 % Rotamer Outliers : 0.06 % 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: 1.16 (0.20), residues: 1954 helix: 1.69 (0.16), residues: 1182 sheet: 0.13 (0.65), residues: 65 loop : -0.72 (0.23), residues: 707 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3908 Ramachandran restraints generated. 1954 Oldfield, 0 Emsley, 1954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.6482 time to fit residues: 99.0125 Evaluate side-chains 92 residues out of total 1761 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 2.391 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.5509 time to fit residues: 3.9853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 47 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 156 optimal weight: 0.0070 chunk 65 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.106735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.076600 restraints weight = 151359.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.079107 restraints weight = 69833.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.080835 restraints weight = 47333.428| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 16024 Z= 0.145 Angle : 0.475 10.370 21715 Z= 0.240 Chirality : 0.034 0.131 2524 Planarity : 0.003 0.047 2739 Dihedral : 4.227 51.282 2131 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.33 % Favored : 96.62 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.19), residues: 1954 helix: 1.75 (0.15), residues: 1180 sheet: 0.17 (0.65), residues: 65 loop : -0.70 (0.23), residues: 709 =============================================================================== Job complete usr+sys time: 4870.19 seconds wall clock time: 88 minutes 36.99 seconds (5316.99 seconds total)