Starting phenix.real_space_refine on Sat Jan 20 13:13:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojk_12954/01_2024/7ojk_12954.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojk_12954/01_2024/7ojk_12954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojk_12954/01_2024/7ojk_12954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojk_12954/01_2024/7ojk_12954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojk_12954/01_2024/7ojk_12954.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojk_12954/01_2024/7ojk_12954.pdb" } resolution = 3.89 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= 0.001 sd= 0.011 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 20 5.49 5 S 91 5.16 5 C 9691 2.51 5 N 2584 2.21 5 O 2929 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 15316 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 14866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1843, 14866 Classifications: {'peptide': 1843} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 62, 'TRANS': 1780} Chain breaks: 12 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 193 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna3p': 8} Chain: "D" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNA': 12} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 9} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2531 SG CYS L 321 44.699 105.525 90.938 1.00135.50 S ATOM 2916 SG CYS L 366 42.614 104.378 93.658 1.00140.11 S Time building chain proxies: 8.35, per 1000 atoms: 0.55 Number of scatterers: 15316 At special positions: 0 Unit cell: (113.97, 126.15, 147.03, 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 91 16.00 P 20 15.00 O 2929 8.00 N 2584 7.00 C 9691 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=0, symmetry=0 Time building additional restraints: 7.18 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L2301 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L 364 " pdb="ZN ZN L2301 " - pdb=" SG CYS L 366 " pdb="ZN ZN L2301 " - pdb=" SG CYS L 321 " 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3528 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 9 sheets defined 55.3% alpha, 3.7% beta 3 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 5.58 Creating SS restraints... Processing helix chain 'L' and resid 1 through 15 removed outlier: 3.578A pdb=" N MET L 5 " --> pdb=" O MET L 1 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 21 No H-bonds generated for 'chain 'L' and resid 19 through 21' Processing helix chain 'L' and resid 22 through 30 Processing helix chain 'L' and resid 34 through 59 Processing helix chain 'L' and resid 68 through 75 Processing helix chain 'L' and resid 112 through 131 removed outlier: 3.636A pdb=" N TYR L 116 " --> pdb=" O PHE L 112 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU L 126 " --> pdb=" O LYS L 122 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP L 129 " --> pdb=" O GLN L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 134 No H-bonds generated for 'chain 'L' and resid 132 through 134' Processing helix chain 'L' and resid 153 through 169 removed outlier: 3.726A pdb=" N THR L 163 " --> pdb=" O LYS L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 176 Processing helix chain 'L' and resid 179 through 188 removed outlier: 3.532A pdb=" N GLU L 188 " --> pdb=" O SER L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 206 Processing helix chain 'L' and resid 214 through 224 removed outlier: 3.864A pdb=" N ILE L 218 " --> pdb=" O TYR L 214 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY L 224 " --> pdb=" O SER L 220 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 251 removed outlier: 4.140A pdb=" N LEU L 236 " --> pdb=" O HIS L 232 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN L 237 " --> pdb=" O GLU L 233 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS L 251 " --> pdb=" O ASN L 247 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 272 Processing helix chain 'L' and resid 284 through 293 removed outlier: 3.882A pdb=" N LYS L 293 " --> pdb=" O ILE L 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 303 removed outlier: 3.534A pdb=" N TYR L 303 " --> pdb=" O LEU L 299 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 336 removed outlier: 3.628A pdb=" N LEU L 336 " --> pdb=" O LYS L 332 " (cutoff:3.500A) Processing helix chain 'L' and resid 345 through 365 removed outlier: 3.738A pdb=" N PHE L 349 " --> pdb=" O LEU L 345 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE L 353 " --> pdb=" O PHE L 349 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR L 362 " --> pdb=" O ILE L 358 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ARG L 363 " --> pdb=" O HIS L 359 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N HIS L 364 " --> pdb=" O ASP L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 405 Processing helix chain 'L' and resid 412 through 433 Processing helix chain 'L' and resid 453 through 459 Processing helix chain 'L' and resid 491 through 506 removed outlier: 4.129A pdb=" N GLU L 495 " --> pdb=" O SER L 491 " (cutoff:3.500A) Processing helix chain 'L' and resid 507 through 509 No H-bonds generated for 'chain 'L' and resid 507 through 509' Processing helix chain 'L' and resid 522 through 527 removed outlier: 3.939A pdb=" N TYR L 526 " --> pdb=" O PRO L 523 " (cutoff:3.500A) Processing helix chain 'L' and resid 589 through 600 removed outlier: 3.816A pdb=" N TRP L 600 " --> pdb=" O THR L 596 " (cutoff:3.500A) Processing helix chain 'L' and resid 604 through 609 removed outlier: 6.017A pdb=" N GLU L 609 " --> pdb=" O GLU L 606 " (cutoff:3.500A) Processing helix chain 'L' and resid 610 through 628 removed outlier: 3.512A pdb=" N ILE L 614 " --> pdb=" O GLN L 610 " (cutoff:3.500A) Processing helix chain 'L' and resid 630 through 632 No H-bonds generated for 'chain 'L' and resid 630 through 632' Processing helix chain 'L' and resid 633 through 648 removed outlier: 3.845A pdb=" N LEU L 637 " --> pdb=" O SER L 633 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU L 640 " --> pdb=" O LEU L 636 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG L 641 " --> pdb=" O LEU L 637 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR L 642 " --> pdb=" O GLN L 638 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE L 643 " --> pdb=" O ASN L 639 " (cutoff:3.500A) Processing helix chain 'L' and resid 656 through 660 Processing helix chain 'L' and resid 667 through 685 Processing helix chain 'L' and resid 691 through 704 removed outlier: 3.985A pdb=" N ARG L 695 " --> pdb=" O MET L 691 " (cutoff:3.500A) Processing helix chain 'L' and resid 716 through 729 removed outlier: 3.991A pdb=" N LYS L 722 " --> pdb=" O THR L 718 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS L 723 " --> pdb=" O ASP L 719 " (cutoff:3.500A) Processing helix chain 'L' and resid 729 through 734 removed outlier: 4.314A pdb=" N GLU L 733 " --> pdb=" O GLU L 729 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE L 734 " --> pdb=" O PRO L 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 729 through 734' Processing helix chain 'L' and resid 746 through 761 removed outlier: 3.678A pdb=" N LEU L 750 " --> pdb=" O THR L 746 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU L 761 " --> pdb=" O ALA L 757 " (cutoff:3.500A) Processing helix chain 'L' and resid 780 through 793 Processing helix chain 'L' and resid 798 through 803 Processing helix chain 'L' and resid 842 through 861 removed outlier: 3.651A pdb=" N LEU L 846 " --> pdb=" O ASP L 842 " (cutoff:3.500A) Processing helix chain 'L' and resid 862 through 865 Processing helix chain 'L' and resid 870 through 884 Processing helix chain 'L' and resid 897 through 905 Processing helix chain 'L' and resid 908 through 925 removed outlier: 3.607A pdb=" N ASP L 912 " --> pdb=" O SER L 908 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU L 916 " --> pdb=" O ASP L 912 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR L 925 " --> pdb=" O ILE L 921 " (cutoff:3.500A) Processing helix chain 'L' and resid 943 through 949 Processing helix chain 'L' and resid 952 through 964 removed outlier: 4.100A pdb=" N ILE L 956 " --> pdb=" O ASN L 952 " (cutoff:3.500A) Processing helix chain 'L' and resid 977 through 991 removed outlier: 3.953A pdb=" N TYR L 981 " --> pdb=" O PRO L 977 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU L 982 " --> pdb=" O GLY L 978 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN L 991 " --> pdb=" O ALA L 987 " (cutoff:3.500A) Processing helix chain 'L' and resid 991 through 999 Processing helix chain 'L' and resid 1014 through 1024 removed outlier: 3.821A pdb=" N PHE L1022 " --> pdb=" O THR L1018 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP L1023 " --> pdb=" O ARG L1019 " (cutoff:3.500A) Processing helix chain 'L' and resid 1025 through 1038 Processing helix chain 'L' and resid 1059 through 1067 removed outlier: 3.841A pdb=" N LEU L1063 " --> pdb=" O ASP L1059 " (cutoff:3.500A) Processing helix chain 'L' and resid 1075 through 1084 removed outlier: 3.553A pdb=" N LEU L1079 " --> pdb=" O ASN L1075 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS L1081 " --> pdb=" O GLU L1077 " (cutoff:3.500A) Processing helix chain 'L' and resid 1092 through 1096 removed outlier: 3.532A pdb=" N LEU L1096 " --> pdb=" O LEU L1093 " (cutoff:3.500A) Processing helix chain 'L' and resid 1137 through 1156 removed outlier: 3.940A pdb=" N LEU L1146 " --> pdb=" O MET L1142 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE L1147 " --> pdb=" O PHE L1143 " (cutoff:3.500A) Processing helix chain 'L' and resid 1168 through 1180 Processing helix chain 'L' and resid 1199 through 1209 removed outlier: 3.613A pdb=" N PHE L1203 " --> pdb=" O CYS L1199 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN L1209 " --> pdb=" O ALA L1205 " (cutoff:3.500A) Processing helix chain 'L' and resid 1218 through 1235 Processing helix chain 'L' and resid 1242 through 1259 removed outlier: 3.698A pdb=" N VAL L1246 " --> pdb=" O PRO L1242 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU L1258 " --> pdb=" O ILE L1254 " (cutoff:3.500A) Processing helix chain 'L' and resid 1267 through 1278 removed outlier: 3.814A pdb=" N ASP L1271 " --> pdb=" O SER L1267 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN L1276 " --> pdb=" O PHE L1272 " (cutoff:3.500A) Processing helix chain 'L' and resid 1297 through 1320 Processing helix chain 'L' and resid 1338 through 1345 removed outlier: 3.787A pdb=" N MET L1345 " --> pdb=" O LEU L1341 " (cutoff:3.500A) Processing helix chain 'L' and resid 1348 through 1366 Processing helix chain 'L' and resid 1396 through 1406 removed outlier: 3.774A pdb=" N PHE L1400 " --> pdb=" O LEU L1396 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N HIS L1406 " --> pdb=" O ALA L1402 " (cutoff:3.500A) Processing helix chain 'L' and resid 1414 through 1429 removed outlier: 4.396A pdb=" N GLU L1418 " --> pdb=" O HIS L1414 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA L1429 " --> pdb=" O ASP L1425 " (cutoff:3.500A) Processing helix chain 'L' and resid 1433 through 1450 removed outlier: 3.704A pdb=" N CYS L1437 " --> pdb=" O PRO L1433 " (cutoff:3.500A) Processing helix chain 'L' and resid 1466 through 1471 removed outlier: 4.080A pdb=" N VAL L1470 " --> pdb=" O VAL L1466 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP L1471 " --> pdb=" O ARG L1467 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1466 through 1471' Processing helix chain 'L' and resid 1475 through 1486 Processing helix chain 'L' and resid 1489 through 1506 removed outlier: 3.531A pdb=" N ILE L1493 " --> pdb=" O ALA L1489 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N SER L1495 " --> pdb=" O GLY L1491 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR L1506 " --> pdb=" O ASN L1502 " (cutoff:3.500A) Processing helix chain 'L' and resid 1524 through 1534 Processing helix chain 'L' and resid 1613 through 1624 removed outlier: 3.934A pdb=" N LEU L1624 " --> pdb=" O LEU L1620 " (cutoff:3.500A) Processing helix chain 'L' and resid 1639 through 1649 removed outlier: 4.191A pdb=" N ILE L1649 " --> pdb=" O LEU L1645 " (cutoff:3.500A) Processing helix chain 'L' and resid 1667 through 1671 Processing helix chain 'L' and resid 1684 through 1699 Processing helix chain 'L' and resid 1700 through 1705 removed outlier: 3.500A pdb=" N VAL L1703 " --> pdb=" O GLY L1700 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU L1704 " --> pdb=" O ALA L1701 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY L1705 " --> pdb=" O TRP L1702 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1700 through 1705' Processing helix chain 'L' and resid 1740 through 1751 Processing helix chain 'L' and resid 1751 through 1757 removed outlier: 3.691A pdb=" N LYS L1757 " --> pdb=" O SER L1753 " (cutoff:3.500A) Processing helix chain 'L' and resid 1759 through 1764 Processing helix chain 'L' and resid 1777 through 1790 Processing helix chain 'L' and resid 1835 through 1852 removed outlier: 3.830A pdb=" N TYR L1850 " --> pdb=" O TYR L1846 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL L1851 " --> pdb=" O PHE L1847 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG L1852 " --> pdb=" O GLU L1848 " (cutoff:3.500A) Processing helix chain 'L' and resid 1878 through 1884 removed outlier: 3.834A pdb=" N LEU L1882 " --> pdb=" O LEU L1879 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY L1883 " --> pdb=" O GLN L1880 " (cutoff:3.500A) Proline residue: L1884 - end of helix Processing helix chain 'L' and resid 1885 through 1892 removed outlier: 3.632A pdb=" N VAL L1889 " --> pdb=" O PHE L1885 " (cutoff:3.500A) Processing helix chain 'L' and resid 1893 through 1896 Processing helix chain 'L' and resid 1902 through 1906 removed outlier: 3.661A pdb=" N LEU L1906 " --> pdb=" O LYS L1903 " (cutoff:3.500A) Processing helix chain 'L' and resid 2102 through 2114 Processing helix chain 'L' and resid 2118 through 2134 Processing helix chain 'L' and resid 2144 through 2152 Processing helix chain 'L' and resid 2155 through 2165 removed outlier: 3.838A pdb=" N VAL L2159 " --> pdb=" O ASN L2155 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 91 through 94 removed outlier: 3.676A pdb=" N LEU L 100 " --> pdb=" O ILE L 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 258 through 260 removed outlier: 3.788A pdb=" N TYR L 651 " --> pdb=" O ILE L1376 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE L1376 " --> pdb=" O TYR L 651 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET L1189 " --> pdb=" O GLN L1333 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLN L1333 " --> pdb=" O MET L1189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP L1325 " --> pdb=" O LEU L1336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 375 through 376 removed outlier: 3.679A pdb=" N PHE L 375 " --> pdb=" O VAL L 383 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL L 383 " --> pdb=" O PHE L 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'L' and resid 536 through 540 Processing sheet with id=AA5, first strand: chain 'L' and resid 826 through 829 Processing sheet with id=AA6, first strand: chain 'L' and resid 1120 through 1125 Processing sheet with id=AA7, first strand: chain 'L' and resid 1653 through 1655 removed outlier: 3.564A pdb=" N TRP L1664 " --> pdb=" O SER L1546 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER L1546 " --> pdb=" O TRP L1664 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 1724 through 1726 removed outlier: 4.063A pdb=" N VAL L1810 " --> pdb=" O PHE L1724 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 1854 through 1855 removed outlier: 3.805A pdb=" N PHE L1854 " --> pdb=" O VAL L2082 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS L2092 " --> pdb=" O GLU L2089 " (cutoff:3.500A) 657 hydrogen bonds defined for protein. 1875 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 8 hydrogen bonds 16 hydrogen bond angles 0 basepair planarities 3 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 5.90 Time building geometry restraints manager: 7.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4753 1.34 - 1.46: 2456 1.46 - 1.58: 8271 1.58 - 1.70: 39 1.70 - 1.81: 139 Bond restraints: 15658 Sorted by residual: bond pdb=" CA ARG L 342 " pdb=" C ARG L 342 " ideal model delta sigma weight residual 1.523 1.542 -0.019 1.34e-02 5.57e+03 2.03e+00 bond pdb=" C SER L 296 " pdb=" N PRO L 297 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.35e+00 bond pdb=" CA THR L 710 " pdb=" CB THR L 710 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.93e-02 2.68e+03 8.72e-01 bond pdb=" CA ARG L 342 " pdb=" CB ARG L 342 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 8.53e-01 bond pdb=" N ARG L 342 " pdb=" CA ARG L 342 " ideal model delta sigma weight residual 1.457 1.469 -0.011 1.29e-02 6.01e+03 7.57e-01 ... (remaining 15653 not shown) Histogram of bond angle deviations from ideal: 99.22 - 106.17: 439 106.17 - 113.13: 8430 113.13 - 120.08: 5547 120.08 - 127.03: 6623 127.03 - 133.98: 187 Bond angle restraints: 21226 Sorted by residual: angle pdb=" C THR L 341 " pdb=" N ARG L 342 " pdb=" CA ARG L 342 " ideal model delta sigma weight residual 121.54 132.71 -11.17 1.91e+00 2.74e-01 3.42e+01 angle pdb=" N ARG L 342 " pdb=" CA ARG L 342 " pdb=" CB ARG L 342 " ideal model delta sigma weight residual 110.49 104.01 6.48 1.69e+00 3.50e-01 1.47e+01 angle pdb=" CA ARG L 342 " pdb=" CB ARG L 342 " pdb=" CG ARG L 342 " ideal model delta sigma weight residual 114.10 121.61 -7.51 2.00e+00 2.50e-01 1.41e+01 angle pdb=" C MET L1189 " pdb=" N ASP L1190 " pdb=" CA ASP L1190 " ideal model delta sigma weight residual 122.45 129.11 -6.66 1.78e+00 3.16e-01 1.40e+01 angle pdb=" N ARG L 342 " pdb=" CA ARG L 342 " pdb=" C ARG L 342 " ideal model delta sigma weight residual 110.80 118.58 -7.78 2.13e+00 2.20e-01 1.33e+01 ... (remaining 21221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.21: 8850 22.21 - 44.42: 583 44.42 - 66.63: 76 66.63 - 88.84: 25 88.84 - 111.04: 2 Dihedral angle restraints: 9536 sinusoidal: 4108 harmonic: 5428 Sorted by residual: dihedral pdb=" CA PHE L 581 " pdb=" C PHE L 581 " pdb=" N PRO L 582 " pdb=" CA PRO L 582 " ideal model delta harmonic sigma weight residual -180.00 -153.84 -26.16 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA TYR L1663 " pdb=" C TYR L1663 " pdb=" N TRP L1664 " pdb=" CA TRP L1664 " ideal model delta harmonic sigma weight residual -180.00 -156.02 -23.98 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ARG L 210 " pdb=" C ARG L 210 " pdb=" N SER L 211 " pdb=" CA SER L 211 " ideal model delta harmonic sigma weight residual 180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 9533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1696 0.036 - 0.073: 521 0.073 - 0.109: 145 0.109 - 0.146: 37 0.146 - 0.182: 4 Chirality restraints: 2403 Sorted by residual: chirality pdb=" CA ILE L1376 " pdb=" N ILE L1376 " pdb=" C ILE L1376 " pdb=" CB ILE L1376 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.29e-01 chirality pdb=" CA ARG L 343 " pdb=" N ARG L 343 " pdb=" C ARG L 343 " pdb=" CB ARG L 343 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CB ILE L2144 " pdb=" CA ILE L2144 " pdb=" CG1 ILE L2144 " pdb=" CG2 ILE L2144 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.08e-01 ... (remaining 2400 not shown) Planarity restraints: 2618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER L 616 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.20e+00 pdb=" C SER L 616 " 0.050 2.00e-02 2.50e+03 pdb=" O SER L 616 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU L 617 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET L 620 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.67e+00 pdb=" C MET L 620 " 0.048 2.00e-02 2.50e+03 pdb=" O MET L 620 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE L 621 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL L1016 " 0.014 2.00e-02 2.50e+03 2.71e-02 7.36e+00 pdb=" C VAL L1016 " -0.047 2.00e-02 2.50e+03 pdb=" O VAL L1016 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA L1017 " 0.016 2.00e-02 2.50e+03 ... (remaining 2615 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 704 2.72 - 3.26: 16229 3.26 - 3.81: 23034 3.81 - 4.35: 27761 4.35 - 4.90: 45356 Nonbonded interactions: 113084 Sorted by model distance: nonbonded pdb=" OD2 ASP L2143 " pdb=" OG SER L2146 " model vdw 2.174 2.440 nonbonded pdb=" OG SER L 384 " pdb=" OE1 GLU L 386 " model vdw 2.182 2.440 nonbonded pdb=" OD1 ASP L 350 " pdb=" OG SER L 377 " model vdw 2.184 2.440 nonbonded pdb=" O LEU L 385 " pdb=" OG1 THR L 388 " model vdw 2.184 2.440 nonbonded pdb=" OH TYR L1476 " pdb=" NH2 ARG L1480 " model vdw 2.187 2.520 ... (remaining 113079 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: 5.240 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: 20.550 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 51.420 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 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 : 0.002 0.027 15658 Z= 0.139 Angle : 0.614 11.741 21226 Z= 0.328 Chirality : 0.040 0.182 2403 Planarity : 0.005 0.053 2618 Dihedral : 14.920 111.045 6008 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 15.24 % Favored : 84.53 % Rotamer: Outliers : 0.06 % Allowed : 1.72 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.16), residues: 1817 helix: -1.57 (0.15), residues: 921 sheet: -3.65 (0.44), residues: 90 loop : -4.24 (0.17), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L1233 HIS 0.008 0.001 HIS L1819 PHE 0.032 0.001 PHE L1458 TYR 0.013 0.001 TYR L1476 ARG 0.011 0.000 ARG L 860 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 1.897 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: L 393 GLU cc_start: 0.8657 (tt0) cc_final: 0.8445 (tp30) REVERT: L 394 LYS cc_start: 0.9263 (tppt) cc_final: 0.8984 (tppt) REVERT: L 442 TYR cc_start: 0.7880 (m-80) cc_final: 0.7632 (m-10) REVERT: L 483 MET cc_start: 0.9032 (mmt) cc_final: 0.8771 (mmm) REVERT: L 692 MET cc_start: 0.7848 (mmm) cc_final: 0.7630 (tpp) REVERT: L 753 MET cc_start: 0.8850 (tpp) cc_final: 0.8582 (tpp) REVERT: L 956 ILE cc_start: 0.9657 (mt) cc_final: 0.9449 (mp) REVERT: L 1060 MET cc_start: 0.7632 (mmm) cc_final: 0.7343 (mmm) REVERT: L 1077 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8102 (mt-10) REVERT: L 1842 MET cc_start: 0.9058 (mmp) cc_final: 0.8720 (mmm) outliers start: 1 outliers final: 0 residues processed: 204 average time/residue: 0.3498 time to fit residues: 99.0989 Evaluate side-chains 121 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 0.0980 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 168 optimal weight: 7.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 76 HIS ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 694 ASN ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1435 HIS L1438 ASN ** L1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15658 Z= 0.199 Angle : 0.638 12.213 21226 Z= 0.318 Chirality : 0.040 0.172 2403 Planarity : 0.004 0.075 2618 Dihedral : 10.439 110.300 2304 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.68 % Favored : 89.21 % Rotamer: Outliers : 0.95 % Allowed : 10.14 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.40 (0.19), residues: 1817 helix: 0.05 (0.17), residues: 926 sheet: -2.99 (0.44), residues: 102 loop : -3.54 (0.19), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L2088 HIS 0.012 0.001 HIS L 76 PHE 0.025 0.002 PHE L1885 TYR 0.013 0.001 TYR L1187 ARG 0.005 0.000 ARG L 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 154 ASP cc_start: 0.8690 (m-30) cc_final: 0.8165 (m-30) REVERT: L 393 GLU cc_start: 0.8652 (tt0) cc_final: 0.8449 (tp30) REVERT: L 394 LYS cc_start: 0.9287 (tppt) cc_final: 0.9009 (tppt) REVERT: L 483 MET cc_start: 0.8943 (mmt) cc_final: 0.8650 (mmm) REVERT: L 692 MET cc_start: 0.7835 (mmm) cc_final: 0.7592 (tpp) REVERT: L 753 MET cc_start: 0.8832 (tpp) cc_final: 0.8539 (tpp) REVERT: L 971 PHE cc_start: 0.8099 (t80) cc_final: 0.7873 (t80) REVERT: L 1885 PHE cc_start: 0.8639 (t80) cc_final: 0.8353 (t80) outliers start: 16 outliers final: 8 residues processed: 143 average time/residue: 0.3247 time to fit residues: 69.6544 Evaluate side-chains 109 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 502 LEU Chi-restraints excluded: chain L residue 513 THR Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 833 THR Chi-restraints excluded: chain L residue 1064 SER Chi-restraints excluded: chain L residue 1084 SER Chi-restraints excluded: chain L residue 1481 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 139 optimal weight: 0.0670 chunk 114 optimal weight: 3.9990 chunk 46 optimal weight: 0.0070 chunk 168 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 149 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 57 optimal weight: 0.0030 chunk 135 optimal weight: 1.9990 overall best weight: 0.5748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 56 ASN ** L 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 401 GLN L 694 ASN ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1407 ASN ** L1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15658 Z= 0.150 Angle : 0.571 10.902 21226 Z= 0.286 Chirality : 0.038 0.221 2403 Planarity : 0.003 0.051 2618 Dihedral : 10.114 111.243 2304 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.14 % Favored : 90.81 % Rotamer: Outliers : 1.30 % Allowed : 11.51 % Favored : 87.19 % 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: -1.64 (0.20), residues: 1817 helix: 0.70 (0.17), residues: 936 sheet: -2.72 (0.46), residues: 103 loop : -3.25 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L2088 HIS 0.006 0.001 HIS L1819 PHE 0.020 0.001 PHE L 292 TYR 0.015 0.001 TYR L 91 ARG 0.010 0.000 ARG L 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 1 MET cc_start: 0.8848 (ppp) cc_final: 0.8440 (tmm) REVERT: L 154 ASP cc_start: 0.8625 (m-30) cc_final: 0.8091 (m-30) REVERT: L 393 GLU cc_start: 0.8634 (tt0) cc_final: 0.8429 (tp30) REVERT: L 394 LYS cc_start: 0.9257 (tppt) cc_final: 0.9004 (tppt) REVERT: L 483 MET cc_start: 0.8846 (mmt) cc_final: 0.8618 (mmm) REVERT: L 684 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8740 (mm) REVERT: L 753 MET cc_start: 0.8873 (tpp) cc_final: 0.8636 (tpp) REVERT: L 1060 MET cc_start: 0.8094 (mmm) cc_final: 0.7861 (mmp) REVERT: L 1871 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7711 (t) REVERT: L 1885 PHE cc_start: 0.8595 (t80) cc_final: 0.8315 (t80) REVERT: L 1901 MET cc_start: 0.4853 (mmm) cc_final: 0.4292 (mmp) outliers start: 22 outliers final: 11 residues processed: 137 average time/residue: 0.3175 time to fit residues: 64.4105 Evaluate side-chains 115 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain L residue 513 THR Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 684 LEU Chi-restraints excluded: chain L residue 1059 ASP Chi-restraints excluded: chain L residue 1458 PHE Chi-restraints excluded: chain L residue 1481 GLN Chi-restraints excluded: chain L residue 1647 SER Chi-restraints excluded: chain L residue 1780 LEU Chi-restraints excluded: chain L residue 1871 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 178 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 694 ASN ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1407 ASN ** L1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1742 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15658 Z= 0.294 Angle : 0.643 14.232 21226 Z= 0.325 Chirality : 0.040 0.162 2403 Planarity : 0.004 0.043 2618 Dihedral : 10.181 112.673 2304 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 2.37 % Allowed : 13.35 % Favored : 84.28 % 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: -1.64 (0.20), residues: 1817 helix: 0.61 (0.17), residues: 936 sheet: -2.58 (0.45), residues: 109 loop : -3.13 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 155 HIS 0.007 0.001 HIS L 364 PHE 0.017 0.002 PHE L 292 TYR 0.012 0.002 TYR L 704 ARG 0.020 0.001 ARG L 363 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 104 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 38 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8787 (mm) REVERT: L 154 ASP cc_start: 0.8750 (m-30) cc_final: 0.8181 (m-30) REVERT: L 393 GLU cc_start: 0.8713 (tt0) cc_final: 0.8489 (tp30) REVERT: L 394 LYS cc_start: 0.9298 (tppt) cc_final: 0.9026 (tppt) REVERT: L 753 MET cc_start: 0.8853 (tpp) cc_final: 0.8600 (tpp) REVERT: L 1871 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7755 (t) REVERT: L 1885 PHE cc_start: 0.8687 (t80) cc_final: 0.8433 (t80) REVERT: L 1901 MET cc_start: 0.5427 (mmm) cc_final: 0.5128 (mmp) outliers start: 40 outliers final: 22 residues processed: 133 average time/residue: 0.2666 time to fit residues: 55.0992 Evaluate side-chains 116 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain L residue 465 VAL Chi-restraints excluded: chain L residue 502 LEU Chi-restraints excluded: chain L residue 513 THR Chi-restraints excluded: chain L residue 620 MET Chi-restraints excluded: chain L residue 713 THR Chi-restraints excluded: chain L residue 833 THR Chi-restraints excluded: chain L residue 882 LEU Chi-restraints excluded: chain L residue 1059 ASP Chi-restraints excluded: chain L residue 1084 SER Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1458 PHE Chi-restraints excluded: chain L residue 1481 GLN Chi-restraints excluded: chain L residue 1693 LEU Chi-restraints excluded: chain L residue 1771 MET Chi-restraints excluded: chain L residue 1780 LEU Chi-restraints excluded: chain L residue 1861 LEU Chi-restraints excluded: chain L residue 1871 THR Chi-restraints excluded: chain L residue 2109 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 3.9990 chunk 101 optimal weight: 0.0770 chunk 2 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 160 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 125 GLN ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15658 Z= 0.155 Angle : 0.575 12.212 21226 Z= 0.286 Chirality : 0.038 0.160 2403 Planarity : 0.003 0.044 2618 Dihedral : 9.938 112.693 2304 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.31 % Favored : 91.63 % Rotamer: Outliers : 1.42 % Allowed : 15.07 % Favored : 83.51 % 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: -1.22 (0.20), residues: 1817 helix: 0.96 (0.18), residues: 939 sheet: -1.78 (0.49), residues: 99 loop : -3.06 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L1547 HIS 0.005 0.001 HIS L1819 PHE 0.029 0.001 PHE L 954 TYR 0.007 0.001 TYR L1663 ARG 0.003 0.000 ARG L 343 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 38 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8650 (mm) REVERT: L 154 ASP cc_start: 0.8649 (m-30) cc_final: 0.8074 (m-30) REVERT: L 393 GLU cc_start: 0.8701 (tt0) cc_final: 0.8483 (tp30) REVERT: L 394 LYS cc_start: 0.9256 (tppt) cc_final: 0.9036 (tppt) REVERT: L 753 MET cc_start: 0.8811 (tpp) cc_final: 0.8562 (tpp) REVERT: L 1030 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: L 1699 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8714 (mt) REVERT: L 1885 PHE cc_start: 0.8722 (t80) cc_final: 0.8449 (t80) REVERT: L 1901 MET cc_start: 0.5287 (mmm) cc_final: 0.4558 (mmp) outliers start: 24 outliers final: 12 residues processed: 124 average time/residue: 0.2751 time to fit residues: 52.3859 Evaluate side-chains 113 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 465 VAL Chi-restraints excluded: chain L residue 502 LEU Chi-restraints excluded: chain L residue 513 THR Chi-restraints excluded: chain L residue 1030 PHE Chi-restraints excluded: chain L residue 1059 ASP Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1458 PHE Chi-restraints excluded: chain L residue 1699 LEU Chi-restraints excluded: chain L residue 1771 MET Chi-restraints excluded: chain L residue 1780 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.5980 chunk 161 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 148 optimal weight: 0.0570 chunk 82 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 694 ASN ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1285 HIS L1461 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15658 Z= 0.172 Angle : 0.555 11.251 21226 Z= 0.278 Chirality : 0.037 0.160 2403 Planarity : 0.003 0.045 2618 Dihedral : 9.874 113.002 2304 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 1.78 % Allowed : 15.18 % Favored : 83.04 % 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: -1.15 (0.20), residues: 1817 helix: 1.00 (0.18), residues: 936 sheet: -2.05 (0.48), residues: 109 loop : -2.94 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 155 HIS 0.004 0.001 HIS L1819 PHE 0.015 0.001 PHE L 421 TYR 0.009 0.001 TYR L1187 ARG 0.003 0.000 ARG L 343 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 98 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 38 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8747 (mm) REVERT: L 154 ASP cc_start: 0.8679 (m-30) cc_final: 0.8112 (m-30) REVERT: L 167 LEU cc_start: 0.9371 (mm) cc_final: 0.9119 (pp) REVERT: L 393 GLU cc_start: 0.8724 (tt0) cc_final: 0.8498 (tp30) REVERT: L 394 LYS cc_start: 0.9261 (tppt) cc_final: 0.9038 (tppt) REVERT: L 442 TYR cc_start: 0.8002 (m-80) cc_final: 0.7735 (m-10) REVERT: L 753 MET cc_start: 0.8809 (tpp) cc_final: 0.8576 (tpp) REVERT: L 1030 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.8038 (m-80) REVERT: L 1699 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8708 (mt) REVERT: L 1885 PHE cc_start: 0.8748 (t80) cc_final: 0.8508 (t80) REVERT: L 1901 MET cc_start: 0.5272 (mmm) cc_final: 0.4576 (mmp) outliers start: 30 outliers final: 19 residues processed: 123 average time/residue: 0.2784 time to fit residues: 52.3717 Evaluate side-chains 116 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain L residue 465 VAL Chi-restraints excluded: chain L residue 502 LEU Chi-restraints excluded: chain L residue 513 THR Chi-restraints excluded: chain L residue 713 THR Chi-restraints excluded: chain L residue 829 VAL Chi-restraints excluded: chain L residue 882 LEU Chi-restraints excluded: chain L residue 963 LEU Chi-restraints excluded: chain L residue 1030 PHE Chi-restraints excluded: chain L residue 1059 ASP Chi-restraints excluded: chain L residue 1084 SER Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1458 PHE Chi-restraints excluded: chain L residue 1699 LEU Chi-restraints excluded: chain L residue 1719 ASN Chi-restraints excluded: chain L residue 1780 LEU Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 101 optimal weight: 0.0770 chunk 130 optimal weight: 0.9980 chunk 150 optimal weight: 0.0370 chunk 99 optimal weight: 0.8980 chunk 178 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 694 ASN ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1276 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 15658 Z= 0.141 Angle : 0.563 15.119 21226 Z= 0.277 Chirality : 0.037 0.155 2403 Planarity : 0.003 0.046 2618 Dihedral : 9.767 113.017 2304 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 1.66 % Allowed : 15.60 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.21), residues: 1817 helix: 1.10 (0.18), residues: 943 sheet: -1.88 (0.48), residues: 109 loop : -2.86 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L1547 HIS 0.003 0.000 HIS L1819 PHE 0.017 0.001 PHE L 971 TYR 0.007 0.001 TYR L1501 ARG 0.003 0.000 ARG L1019 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 107 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 38 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8449 (mm) REVERT: L 154 ASP cc_start: 0.8611 (m-30) cc_final: 0.8044 (m-30) REVERT: L 167 LEU cc_start: 0.9357 (mm) cc_final: 0.9120 (pp) REVERT: L 393 GLU cc_start: 0.8707 (tt0) cc_final: 0.8485 (tp30) REVERT: L 394 LYS cc_start: 0.9229 (tppt) cc_final: 0.9021 (tppt) REVERT: L 442 TYR cc_start: 0.7971 (m-80) cc_final: 0.7730 (m-10) REVERT: L 1030 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.8063 (m-80) REVERT: L 1699 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8698 (mt) REVERT: L 1885 PHE cc_start: 0.8735 (t80) cc_final: 0.8496 (t80) REVERT: L 1901 MET cc_start: 0.5437 (mmm) cc_final: 0.4826 (mmp) REVERT: L 2128 MET cc_start: 0.8609 (tmm) cc_final: 0.8256 (ppp) REVERT: L 2137 MET cc_start: 0.2139 (ptp) cc_final: 0.1813 (ptp) outliers start: 28 outliers final: 17 residues processed: 129 average time/residue: 0.2895 time to fit residues: 57.1333 Evaluate side-chains 114 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain L residue 465 VAL Chi-restraints excluded: chain L residue 502 LEU Chi-restraints excluded: chain L residue 513 THR Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 829 VAL Chi-restraints excluded: chain L residue 1030 PHE Chi-restraints excluded: chain L residue 1059 ASP Chi-restraints excluded: chain L residue 1084 SER Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1458 PHE Chi-restraints excluded: chain L residue 1699 LEU Chi-restraints excluded: chain L residue 1780 LEU Chi-restraints excluded: chain L residue 2118 LEU Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 694 ASN ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1313 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15658 Z= 0.242 Angle : 0.597 15.006 21226 Z= 0.300 Chirality : 0.038 0.164 2403 Planarity : 0.003 0.048 2618 Dihedral : 9.894 113.746 2304 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 1.90 % Allowed : 16.07 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.20), residues: 1817 helix: 1.04 (0.18), residues: 941 sheet: -1.84 (0.48), residues: 109 loop : -2.89 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L1194 HIS 0.004 0.001 HIS L 652 PHE 0.034 0.002 PHE L 481 TYR 0.014 0.001 TYR L1187 ARG 0.003 0.000 ARG L2084 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 98 time to evaluate : 2.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 38 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8572 (mm) REVERT: L 154 ASP cc_start: 0.8637 (m-30) cc_final: 0.8084 (m-30) REVERT: L 167 LEU cc_start: 0.9367 (mm) cc_final: 0.9099 (pp) REVERT: L 192 MET cc_start: 0.8146 (tmm) cc_final: 0.7746 (tmm) REVERT: L 393 GLU cc_start: 0.8695 (tt0) cc_final: 0.8487 (tp30) REVERT: L 394 LYS cc_start: 0.9266 (tppt) cc_final: 0.9039 (tppt) REVERT: L 420 MET cc_start: 0.8575 (tmm) cc_final: 0.8372 (tmm) REVERT: L 1060 MET cc_start: 0.7888 (mmp) cc_final: 0.7556 (mmp) REVERT: L 1699 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8698 (mt) REVERT: L 1885 PHE cc_start: 0.8725 (t80) cc_final: 0.8421 (t80) REVERT: L 1901 MET cc_start: 0.5643 (mmm) cc_final: 0.5232 (mmm) outliers start: 32 outliers final: 26 residues processed: 124 average time/residue: 0.2513 time to fit residues: 50.0201 Evaluate side-chains 119 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain L residue 465 VAL Chi-restraints excluded: chain L residue 502 LEU Chi-restraints excluded: chain L residue 513 THR Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 713 THR Chi-restraints excluded: chain L residue 723 CYS Chi-restraints excluded: chain L residue 829 VAL Chi-restraints excluded: chain L residue 963 LEU Chi-restraints excluded: chain L residue 1059 ASP Chi-restraints excluded: chain L residue 1084 SER Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1374 SER Chi-restraints excluded: chain L residue 1458 PHE Chi-restraints excluded: chain L residue 1633 ASN Chi-restraints excluded: chain L residue 1693 LEU Chi-restraints excluded: chain L residue 1699 LEU Chi-restraints excluded: chain L residue 1719 ASN Chi-restraints excluded: chain L residue 1780 LEU Chi-restraints excluded: chain L residue 1864 PHE Chi-restraints excluded: chain L residue 2118 LEU Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 130 optimal weight: 0.0870 chunk 50 optimal weight: 0.6980 chunk 150 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 324 GLN L 694 ASN ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15658 Z= 0.181 Angle : 0.578 13.295 21226 Z= 0.289 Chirality : 0.038 0.159 2403 Planarity : 0.003 0.048 2618 Dihedral : 9.863 113.715 2304 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 1.72 % Allowed : 16.43 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.21), residues: 1817 helix: 1.09 (0.18), residues: 944 sheet: -1.79 (0.48), residues: 109 loop : -2.85 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 326 HIS 0.003 0.001 HIS L 652 PHE 0.045 0.001 PHE L 421 TYR 0.009 0.001 TYR L 214 ARG 0.003 0.000 ARG L2084 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 97 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 38 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8460 (mm) REVERT: L 154 ASP cc_start: 0.8604 (m-30) cc_final: 0.8043 (m-30) REVERT: L 167 LEU cc_start: 0.9359 (mm) cc_final: 0.9093 (pp) REVERT: L 394 LYS cc_start: 0.9250 (tppt) cc_final: 0.9035 (tppt) REVERT: L 442 TYR cc_start: 0.8032 (m-80) cc_final: 0.7769 (m-10) REVERT: L 650 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8309 (t0) REVERT: L 1092 MET cc_start: 0.7876 (tpt) cc_final: 0.7540 (mtt) REVERT: L 1699 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8611 (mt) REVERT: L 1885 PHE cc_start: 0.8718 (t80) cc_final: 0.8433 (t80) REVERT: L 1901 MET cc_start: 0.5625 (mmm) cc_final: 0.5021 (mmp) outliers start: 29 outliers final: 22 residues processed: 121 average time/residue: 0.2656 time to fit residues: 49.7530 Evaluate side-chains 117 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain L residue 465 VAL Chi-restraints excluded: chain L residue 502 LEU Chi-restraints excluded: chain L residue 513 THR Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 650 ASP Chi-restraints excluded: chain L residue 713 THR Chi-restraints excluded: chain L residue 723 CYS Chi-restraints excluded: chain L residue 829 VAL Chi-restraints excluded: chain L residue 882 LEU Chi-restraints excluded: chain L residue 1059 ASP Chi-restraints excluded: chain L residue 1084 SER Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1458 PHE Chi-restraints excluded: chain L residue 1699 LEU Chi-restraints excluded: chain L residue 1719 ASN Chi-restraints excluded: chain L residue 1780 LEU Chi-restraints excluded: chain L residue 2118 LEU Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 169 optimal weight: 8.9990 chunk 146 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 694 ASN ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15658 Z= 0.209 Angle : 0.590 11.416 21226 Z= 0.297 Chirality : 0.038 0.151 2403 Planarity : 0.003 0.047 2618 Dihedral : 9.902 113.828 2304 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 1.72 % Allowed : 16.67 % Favored : 81.61 % 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: -1.00 (0.20), residues: 1817 helix: 1.05 (0.18), residues: 943 sheet: -1.68 (0.49), residues: 109 loop : -2.84 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L1194 HIS 0.004 0.001 HIS L 652 PHE 0.049 0.002 PHE L 421 TYR 0.011 0.001 TYR L1187 ARG 0.004 0.000 ARG L 716 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3634 Ramachandran restraints generated. 1817 Oldfield, 0 Emsley, 1817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 97 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 38 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8468 (mm) REVERT: L 154 ASP cc_start: 0.8614 (m-30) cc_final: 0.8054 (m-30) REVERT: L 167 LEU cc_start: 0.9354 (mm) cc_final: 0.9096 (pp) REVERT: L 650 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8351 (t0) REVERT: L 1092 MET cc_start: 0.8017 (tpt) cc_final: 0.7522 (mtm) REVERT: L 1885 PHE cc_start: 0.8710 (t80) cc_final: 0.8440 (t80) REVERT: L 1901 MET cc_start: 0.5755 (mmm) cc_final: 0.5347 (mmm) outliers start: 29 outliers final: 24 residues processed: 120 average time/residue: 0.2638 time to fit residues: 49.4837 Evaluate side-chains 120 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 94 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain L residue 205 VAL Chi-restraints excluded: chain L residue 254 ILE Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain L residue 465 VAL Chi-restraints excluded: chain L residue 502 LEU Chi-restraints excluded: chain L residue 513 THR Chi-restraints excluded: chain L residue 540 LEU Chi-restraints excluded: chain L residue 650 ASP Chi-restraints excluded: chain L residue 713 THR Chi-restraints excluded: chain L residue 723 CYS Chi-restraints excluded: chain L residue 829 VAL Chi-restraints excluded: chain L residue 882 LEU Chi-restraints excluded: chain L residue 963 LEU Chi-restraints excluded: chain L residue 1059 ASP Chi-restraints excluded: chain L residue 1084 SER Chi-restraints excluded: chain L residue 1300 THR Chi-restraints excluded: chain L residue 1328 THR Chi-restraints excluded: chain L residue 1458 PHE Chi-restraints excluded: chain L residue 1633 ASN Chi-restraints excluded: chain L residue 1719 ASN Chi-restraints excluded: chain L residue 1780 LEU Chi-restraints excluded: chain L residue 2118 LEU Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 40 optimal weight: 0.9990 chunk 146 optimal weight: 0.1980 chunk 61 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 694 ASN ** L 740 ASN ** 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 = 0.3715 r_free = 0.3715 target = 0.080725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.056788 restraints weight = 64057.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.058351 restraints weight = 35935.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.058918 restraints weight = 22230.669| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15658 Z= 0.155 Angle : 0.581 12.078 21226 Z= 0.290 Chirality : 0.038 0.245 2403 Planarity : 0.003 0.047 2618 Dihedral : 9.844 113.513 2304 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 1.48 % Allowed : 17.02 % Favored : 81.49 % 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: -0.88 (0.21), residues: 1817 helix: 1.14 (0.18), residues: 943 sheet: -1.65 (0.48), residues: 109 loop : -2.78 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L1194 HIS 0.003 0.001 HIS L 652 PHE 0.046 0.001 PHE L 421 TYR 0.008 0.001 TYR L 214 ARG 0.004 0.000 ARG L 716 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2974.22 seconds wall clock time: 55 minutes 43.42 seconds (3343.42 seconds total)