Starting phenix.real_space_refine on Tue Apr 9 04:30:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojk_12954/04_2024/7ojk_12954.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojk_12954/04_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_12954/04_2024/7ojk_12954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojk_12954/04_2024/7ojk_12954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojk_12954/04_2024/7ojk_12954.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojk_12954/04_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 8.79, per 1000 atoms: 0.57 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: 6.50 Conformation dependent library (CDL) restraints added in 2.7 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: 5.41 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: 6.53 Time building geometry restraints manager: 6.96 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: 8854 22.21 - 44.42: 587 44.42 - 66.63: 84 66.63 - 88.84: 25 88.84 - 111.04: 2 Dihedral angle restraints: 9552 sinusoidal: 4124 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 9549 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: 4.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 20.620 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 51.490 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.310 ------------------------------------------------------------------------------- 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 : 15.072 111.045 6024 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 : 2.009 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: 0.3659 time to fit residues: 102.8101 Evaluate side-chains 121 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.810 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1704 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= 0.200 Angle : 0.639 11.510 21226 Z= 0.319 Chirality : 0.040 0.169 2403 Planarity : 0.004 0.076 2618 Dihedral : 10.998 110.163 2320 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.73 % Favored : 89.16 % Rotamer: Outliers : 0.89 % Allowed : 9.85 % Favored : 89.26 % 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: -2.46 (0.19), residues: 1817 helix: -0.01 (0.17), residues: 926 sheet: -3.01 (0.44), residues: 102 loop : -3.58 (0.19), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP L2088 HIS 0.013 0.001 HIS L 76 PHE 0.027 0.002 PHE L1885 TYR 0.013 0.001 TYR L1187 ARG 0.004 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: 15 poor density : 133 time to evaluate : 1.790 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: 0.8706 (m-30) cc_final: 0.8185 (m-30) REVERT: L 393 GLU cc_start: 0.8658 (tt0) cc_final: 0.8452 (tp30) REVERT: L 394 LYS cc_start: 0.9288 (tppt) cc_final: 0.9011 (tppt) REVERT: L 483 MET cc_start: 0.8941 (mmt) cc_final: 0.8643 (mmm) REVERT: L 684 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8792 (mm) REVERT: L 692 MET cc_start: 0.7845 (mmm) cc_final: 0.7626 (tpp) REVERT: L 753 MET cc_start: 0.8824 (tpp) cc_final: 0.8523 (tpp) REVERT: L 1885 PHE cc_start: 0.8659 (t80) cc_final: 0.8244 (t80) REVERT: L 1901 MET cc_start: 0.5180 (mmm) cc_final: 0.4839 (mmp) outliers start: 15 outliers final: 8 residues processed: 144 average time/residue: 0.3368 time to fit residues: 72.0895 Evaluate side-chains 110 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 2.035 ------------------------------------------------------------------------------- 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 684 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: 3.9990 chunk 52 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 46 optimal weight: 0.0030 chunk 168 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15658 Z= 0.160 Angle : 0.577 11.442 21226 Z= 0.289 Chirality : 0.038 0.172 2403 Planarity : 0.003 0.051 2618 Dihedral : 10.696 110.863 2320 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.63 % Favored : 90.31 % Rotamer: Outliers : 1.30 % Allowed : 11.63 % Favored : 87.07 % 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: -1.74 (0.20), residues: 1817 helix: 0.62 (0.17), residues: 936 sheet: -2.79 (0.46), residues: 103 loop : -3.30 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L2088 HIS 0.006 0.001 HIS L1819 PHE 0.019 0.001 PHE L 292 TYR 0.013 0.001 TYR L 91 ARG 0.010 0.000 ARG L 920 *********************** 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 139 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 1.930 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: 0.8865 (ppp) cc_final: 0.8455 (tmm) REVERT: L 154 ASP cc_start: 0.8639 (m-30) cc_final: 0.8117 (m-30) REVERT: L 394 LYS cc_start: 0.9256 (tppt) cc_final: 0.8996 (tppt) REVERT: L 483 MET cc_start: 0.8881 (mmt) cc_final: 0.8627 (mmm) REVERT: L 753 MET cc_start: 0.8857 (tpp) cc_final: 0.8593 (tpp) REVERT: L 1060 MET cc_start: 0.8099 (mmm) cc_final: 0.7890 (mmp) REVERT: L 1871 THR cc_start: 0.8017 (OUTLIER) cc_final: 0.7670 (t) REVERT: L 1885 PHE cc_start: 0.8666 (t80) cc_final: 0.8389 (t80) outliers start: 22 outliers final: 12 residues processed: 134 average time/residue: 0.2976 time to fit residues: 60.0603 Evaluate side-chains 114 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 2.466 ------------------------------------------------------------------------------- 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 833 THR 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: 0.9980 chunk 18 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 178 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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** L1285 HIS L1407 ASN ** L1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1742 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15658 Z= 0.267 Angle : 0.620 11.609 21226 Z= 0.314 Chirality : 0.040 0.248 2403 Planarity : 0.004 0.043 2618 Dihedral : 10.676 112.203 2320 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.08 % Allowed : 13.46 % Favored : 84.46 % 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: -1.63 (0.20), residues: 1817 helix: 0.62 (0.17), residues: 936 sheet: -2.59 (0.45), residues: 109 loop : -3.14 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 155 HIS 0.006 0.001 HIS L1819 PHE 0.017 0.002 PHE L 292 TYR 0.012 0.001 TYR L 704 ARG 0.009 0.000 ARG L 716 *********************** 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 141 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 106 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 38 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8801 (mm) REVERT: L 154 ASP cc_start: 0.8740 (m-30) cc_final: 0.8100 (m-30) REVERT: L 483 MET cc_start: 0.8825 (mmt) cc_final: 0.8578 (mmm) REVERT: L 753 MET cc_start: 0.8850 (tpp) cc_final: 0.8603 (tpp) REVERT: L 971 PHE cc_start: 0.8062 (t80) cc_final: 0.7848 (t80) REVERT: L 1060 MET cc_start: 0.8133 (mmm) cc_final: 0.7710 (tpp) REVERT: L 1871 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7713 (t) REVERT: L 1885 PHE cc_start: 0.8688 (t80) cc_final: 0.8400 (t80) REVERT: L 1901 MET cc_start: 0.5328 (mmm) cc_final: 0.4842 (mmp) outliers start: 35 outliers final: 20 residues processed: 132 average time/residue: 0.3086 time to fit residues: 62.6923 Evaluate side-chains 118 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 1.858 ------------------------------------------------------------------------------- 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 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 833 THR 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 1481 GLN Chi-restraints excluded: chain L residue 1628 CYS Chi-restraints excluded: chain L residue 1693 LEU Chi-restraints excluded: chain L residue 1780 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: 4.9990 chunk 101 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 56 ASN ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1276 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: 0.8244 moved from start: 0.2995 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= 0.232 Angle : 0.611 15.888 21226 Z= 0.305 Chirality : 0.038 0.156 2403 Planarity : 0.003 0.044 2618 Dihedral : 10.598 112.553 2320 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.63 % Favored : 90.31 % Rotamer: Outliers : 2.14 % Allowed : 14.59 % Favored : 83.27 % 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: -1.46 (0.20), residues: 1817 helix: 0.74 (0.17), residues: 937 sheet: -2.38 (0.46), residues: 109 loop : -3.07 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 155 HIS 0.006 0.001 HIS L1819 PHE 0.028 0.001 PHE L 954 TYR 0.011 0.001 TYR L 214 ARG 0.004 0.000 ARG L 920 *********************** 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 140 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 104 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 38 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8789 (mm) REVERT: L 154 ASP cc_start: 0.8687 (m-30) cc_final: 0.8133 (m-30) REVERT: L 753 MET cc_start: 0.8823 (tpp) cc_final: 0.8620 (tpp) REVERT: L 856 GLU cc_start: 0.8559 (tt0) cc_final: 0.8348 (tt0) REVERT: L 1030 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7956 (m-80) REVERT: L 1060 MET cc_start: 0.8064 (mmm) cc_final: 0.7802 (mmp) REVERT: L 1699 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8751 (mt) REVERT: L 1885 PHE cc_start: 0.8693 (t80) cc_final: 0.8462 (t80) outliers start: 36 outliers final: 22 residues processed: 135 average time/residue: 0.2703 time to fit residues: 58.1897 Evaluate side-chains 117 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 1.987 ------------------------------------------------------------------------------- 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 833 THR 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 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 1699 LEU Chi-restraints excluded: chain L residue 1771 MET Chi-restraints excluded: chain L residue 1780 LEU Chi-restraints excluded: chain L residue 2109 PHE Chi-restraints excluded: chain L residue 2157 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 178 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15658 Z= 0.182 Angle : 0.567 12.362 21226 Z= 0.285 Chirality : 0.038 0.162 2403 Planarity : 0.003 0.045 2618 Dihedral : 10.470 112.791 2320 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 1.66 % Allowed : 16.07 % Favored : 82.27 % 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: -1.24 (0.20), residues: 1817 helix: 0.92 (0.18), residues: 934 sheet: -1.66 (0.50), residues: 99 loop : -3.03 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 155 HIS 0.005 0.001 HIS L1819 PHE 0.017 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 124 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 96 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 38 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8823 (mm) REVERT: L 154 ASP cc_start: 0.8640 (m-30) cc_final: 0.8069 (m-30) REVERT: L 753 MET cc_start: 0.8788 (tpp) cc_final: 0.8585 (tpp) REVERT: L 1030 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.8032 (m-80) REVERT: L 1060 MET cc_start: 0.8084 (mmm) cc_final: 0.7828 (mmp) REVERT: L 1699 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8745 (mt) REVERT: L 1885 PHE cc_start: 0.8706 (t80) cc_final: 0.8505 (t80) outliers start: 28 outliers final: 19 residues processed: 119 average time/residue: 0.2844 time to fit residues: 52.2329 Evaluate side-chains 111 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 2.000 ------------------------------------------------------------------------------- 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 540 LEU 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 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 1481 GLN Chi-restraints excluded: chain L residue 1693 LEU Chi-restraints excluded: chain L residue 1699 LEU Chi-restraints excluded: chain L residue 1780 LEU Chi-restraints excluded: chain L residue 2118 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 150 optimal weight: 0.4980 chunk 99 optimal weight: 0.8980 chunk 178 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 108 optimal weight: 0.0870 chunk 82 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 305 ASN ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1461 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 15658 Z= 0.157 Angle : 0.570 15.120 21226 Z= 0.282 Chirality : 0.037 0.159 2403 Planarity : 0.003 0.046 2618 Dihedral : 10.376 112.910 2320 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.75 % Favored : 91.19 % Rotamer: Outliers : 2.02 % Allowed : 16.43 % Favored : 81.55 % 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: -1.09 (0.20), residues: 1817 helix: 1.03 (0.18), residues: 939 sheet: -1.50 (0.50), residues: 99 loop : -2.98 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L1194 HIS 0.004 0.001 HIS L1819 PHE 0.012 0.001 PHE L 421 TYR 0.008 0.001 TYR L 214 ARG 0.004 0.000 ARG L 342 *********************** 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 132 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 98 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 38 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8861 (mm) REVERT: L 154 ASP cc_start: 0.8618 (m-30) cc_final: 0.8056 (m-30) REVERT: L 442 TYR cc_start: 0.8005 (m-80) cc_final: 0.7730 (m-10) REVERT: L 650 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.8308 (t0) REVERT: L 753 MET cc_start: 0.8772 (tpp) cc_final: 0.8566 (tpp) REVERT: L 1030 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.8046 (m-80) REVERT: L 1060 MET cc_start: 0.8100 (mmm) cc_final: 0.7842 (mmp) REVERT: L 1699 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8709 (mt) outliers start: 34 outliers final: 21 residues processed: 124 average time/residue: 0.2712 time to fit residues: 53.3912 Evaluate side-chains 114 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 89 time to evaluate : 1.883 ------------------------------------------------------------------------------- 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 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 829 VAL Chi-restraints excluded: chain L residue 856 GLU 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 1481 GLN Chi-restraints excluded: chain L residue 1633 ASN Chi-restraints excluded: chain L residue 1647 SER Chi-restraints excluded: chain L residue 1699 LEU Chi-restraints excluded: chain L residue 1780 LEU Chi-restraints excluded: chain L residue 2144 ILE 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: 1.9990 chunk 106 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 0.4980 chunk 88 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15658 Z= 0.165 Angle : 0.585 15.648 21226 Z= 0.289 Chirality : 0.037 0.159 2403 Planarity : 0.003 0.046 2618 Dihedral : 10.352 113.070 2320 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 2.08 % Allowed : 16.55 % Favored : 81.38 % 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: 1.08 (0.18), residues: 944 sheet: -1.85 (0.48), residues: 109 loop : -2.88 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L1194 HIS 0.003 0.001 HIS L1819 PHE 0.037 0.001 PHE L 954 TYR 0.014 0.001 TYR L1187 ARG 0.006 0.000 ARG L1899 *********************** 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: 35 poor density : 95 time to evaluate : 1.928 Fit side-chains revert: symmetry clash REVERT: L 38 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8510 (mm) REVERT: L 144 ARG cc_start: 0.9394 (mmp-170) cc_final: 0.9176 (mmp80) REVERT: L 154 ASP cc_start: 0.8599 (m-30) cc_final: 0.8030 (m-30) REVERT: L 192 MET cc_start: 0.7619 (tmm) cc_final: 0.7208 (tmm) REVERT: L 420 MET cc_start: 0.8557 (tmm) cc_final: 0.8356 (tmm) REVERT: L 442 TYR cc_start: 0.8003 (m-80) cc_final: 0.7745 (m-10) REVERT: L 650 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8313 (t0) REVERT: L 753 MET cc_start: 0.8771 (tpp) cc_final: 0.8567 (tpp) REVERT: L 1060 MET cc_start: 0.8138 (mmm) cc_final: 0.7749 (tpp) REVERT: L 1699 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8705 (mt) REVERT: L 2128 MET cc_start: 0.8586 (tmm) cc_final: 0.8239 (ppp) outliers start: 35 outliers final: 26 residues processed: 122 average time/residue: 0.2571 time to fit residues: 49.7633 Evaluate side-chains 120 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 91 time to evaluate : 2.187 ------------------------------------------------------------------------------- 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 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 1481 GLN Chi-restraints excluded: chain L residue 1633 ASN Chi-restraints excluded: chain L residue 1647 SER 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 2144 ILE 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: 10.0000 chunk 155 optimal weight: 0.6980 chunk 166 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 157 optimal weight: 0.5980 chunk 165 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** ** L1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1313 ASN ** L1869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15658 Z= 0.163 Angle : 0.585 14.375 21226 Z= 0.290 Chirality : 0.037 0.155 2403 Planarity : 0.003 0.047 2618 Dihedral : 10.328 113.241 2320 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 2.02 % Allowed : 16.61 % Favored : 81.38 % 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: -0.93 (0.21), residues: 1817 helix: 1.11 (0.18), residues: 945 sheet: -1.79 (0.48), residues: 109 loop : -2.82 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L1194 HIS 0.003 0.001 HIS L 652 PHE 0.040 0.001 PHE L 954 TYR 0.008 0.001 TYR L 214 ARG 0.003 0.000 ARG L1899 *********************** 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 127 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 93 time to evaluate : 1.995 Fit side-chains REVERT: L 38 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8531 (mm) REVERT: L 144 ARG cc_start: 0.9392 (mmp-170) cc_final: 0.9177 (mmp80) REVERT: L 154 ASP cc_start: 0.8611 (m-30) cc_final: 0.8056 (m-30) REVERT: L 192 MET cc_start: 0.7696 (tmm) cc_final: 0.7305 (tmm) REVERT: L 442 TYR cc_start: 0.7987 (m-80) cc_final: 0.7735 (m-10) REVERT: L 650 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8290 (t0) REVERT: L 753 MET cc_start: 0.8762 (tpp) cc_final: 0.8558 (tpp) REVERT: L 1060 MET cc_start: 0.8190 (mmm) cc_final: 0.7751 (tpp) REVERT: L 1699 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8639 (mt) outliers start: 34 outliers final: 26 residues processed: 119 average time/residue: 0.2574 time to fit residues: 49.2536 Evaluate side-chains 119 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 90 time to evaluate : 1.793 ------------------------------------------------------------------------------- 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 1481 GLN Chi-restraints excluded: chain L residue 1633 ASN Chi-restraints excluded: chain L residue 1647 SER 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: 7.9990 chunk 107 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 184 optimal weight: 6.9990 chunk 169 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** ** L1869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15658 Z= 0.180 Angle : 0.605 13.915 21226 Z= 0.301 Chirality : 0.038 0.162 2403 Planarity : 0.003 0.048 2618 Dihedral : 10.335 113.386 2320 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 1.72 % Allowed : 17.08 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.20), residues: 1817 helix: 1.10 (0.18), residues: 946 sheet: -1.76 (0.48), residues: 109 loop : -2.78 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L1194 HIS 0.003 0.001 HIS L 652 PHE 0.045 0.001 PHE L 954 TYR 0.016 0.001 TYR L1187 ARG 0.002 0.000 ARG L2084 ********************** 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 123 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 94 time to evaluate : 1.915 Fit side-chains revert: symmetry clash REVERT: L 38 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8376 (mm) REVERT: L 154 ASP cc_start: 0.8600 (m-30) cc_final: 0.8040 (m-30) REVERT: L 192 MET cc_start: 0.7709 (tmm) cc_final: 0.7324 (tmm) REVERT: L 442 TYR cc_start: 0.8009 (m-80) cc_final: 0.7734 (m-10) REVERT: L 650 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8299 (t0) REVERT: L 753 MET cc_start: 0.8756 (tpp) cc_final: 0.8548 (tpp) REVERT: L 1060 MET cc_start: 0.8194 (mmm) cc_final: 0.7772 (tpp) outliers start: 29 outliers final: 26 residues processed: 117 average time/residue: 0.2377 time to fit residues: 45.8496 Evaluate side-chains 120 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 1.888 ------------------------------------------------------------------------------- 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 1481 GLN Chi-restraints excluded: chain L residue 1633 ASN Chi-restraints excluded: chain L residue 1647 SER 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: 0.5980 chunk 44 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 146 optimal weight: 0.0050 chunk 61 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 ** L1869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.081046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.057159 restraints weight = 63756.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.059119 restraints weight = 35889.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.059539 restraints weight = 20641.057| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15658 Z= 0.156 Angle : 0.592 13.499 21226 Z= 0.294 Chirality : 0.037 0.190 2403 Planarity : 0.003 0.047 2618 Dihedral : 10.314 113.273 2320 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 1.66 % Allowed : 17.08 % Favored : 81.26 % 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: -0.85 (0.21), residues: 1817 helix: 1.17 (0.18), residues: 942 sheet: -1.68 (0.48), residues: 109 loop : -2.75 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L1194 HIS 0.003 0.000 HIS L 652 PHE 0.046 0.001 PHE L 954 TYR 0.008 0.001 TYR L1501 ARG 0.002 0.000 ARG L2084 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3042.35 seconds wall clock time: 57 minutes 40.47 seconds (3460.47 seconds total)