Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 7 19:23:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojk_12954/10_2023/7ojk_12954.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojk_12954/10_2023/7ojk_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_12954/10_2023/7ojk_12954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojk_12954/10_2023/7ojk_12954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojk_12954/10_2023/7ojk_12954.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ojk_12954/10_2023/7ojk_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-1.21rc1-5097/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: 8.40, 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: 5.97 Conformation dependent library (CDL) restraints added in 1.9 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: 4.60 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: 5.49 Time building geometry restraints manager: 6.49 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: 8828 22.21 - 44.42: 577 44.42 - 66.63: 43 66.63 - 88.84: 20 88.84 - 111.04: 2 Dihedral angle restraints: 9470 sinusoidal: 4042 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 9467 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: 4.910 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: 20.890 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 45.340 Find NCS groups from input model: 0.390 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.740 ------------------------------------------------------------------------------- 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 : 14.158 111.045 5942 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 *********************** 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 : 1.731 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 outliers start: 1 outliers final: 0 residues processed: 204 average time/residue: 0.3594 time to fit residues: 101.9593 Evaluate side-chains 117 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.794 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5495 ------------------------------------------------------------------------------- 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: 3.9990 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 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: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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: 0.8212 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15658 Z= 0.240 Angle : 0.657 12.249 21226 Z= 0.330 Chirality : 0.040 0.172 2403 Planarity : 0.004 0.074 2618 Dihedral : 7.271 110.258 2238 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.06 % Favored : 88.83 % Rotamer: Outliers : 0.95 % Allowed : 10.79 % Favored : 88.26 % 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: -2.48 (0.19), residues: 1817 helix: -0.03 (0.17), residues: 921 sheet: -3.04 (0.44), residues: 102 loop : -3.55 (0.19), residues: 794 *********************** 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 146 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 141 average time/residue: 0.2981 time to fit residues: 62.4646 Evaluate side-chains 106 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 1.881 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1431 time to fit residues: 4.5975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 114 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 chunk 181 optimal weight: 0.0030 chunk 149 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 chunk 57 optimal weight: 0.0270 chunk 135 optimal weight: 0.9980 overall best weight: 0.4848 ------------------------------------------------------------------------------- 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** L1285 HIS 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: 0.8162 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15658 Z= 0.147 Angle : 0.582 11.561 21226 Z= 0.291 Chirality : 0.038 0.216 2403 Planarity : 0.003 0.051 2618 Dihedral : 6.911 111.134 2238 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.08 % Favored : 90.86 % Rotamer: Outliers : 1.07 % Allowed : 12.22 % Favored : 86.71 % 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: -1.68 (0.20), residues: 1817 helix: 0.62 (0.17), residues: 936 sheet: -2.46 (0.47), residues: 96 loop : -3.25 (0.20), residues: 785 *********************** 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 134 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 129 average time/residue: 0.2908 time to fit residues: 57.0976 Evaluate side-chains 112 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 1.686 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1396 time to fit residues: 4.3787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 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: 0.8278 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15658 Z= 0.329 Angle : 0.672 15.469 21226 Z= 0.339 Chirality : 0.041 0.189 2403 Planarity : 0.004 0.042 2618 Dihedral : 7.146 112.462 2238 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.23 % Favored : 88.72 % Rotamer: Outliers : 1.60 % Allowed : 14.29 % Favored : 84.10 % 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: -1.77 (0.20), residues: 1817 helix: 0.47 (0.17), residues: 938 sheet: -2.63 (0.45), residues: 109 loop : -3.17 (0.21), residues: 770 *********************** 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 129 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 102 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 123 average time/residue: 0.2887 time to fit residues: 54.8149 Evaluate side-chains 102 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 1.936 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1481 time to fit residues: 6.0121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0370 chunk 2 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 56 ASN 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** ** L1461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15658 Z= 0.185 Angle : 0.589 12.131 21226 Z= 0.295 Chirality : 0.038 0.155 2403 Planarity : 0.003 0.043 2618 Dihedral : 6.854 112.667 2238 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.75 % Favored : 91.19 % Rotamer: Outliers : 1.01 % Allowed : 15.78 % Favored : 83.21 % 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: -1.40 (0.20), residues: 1817 helix: 0.77 (0.17), residues: 940 sheet: -2.30 (0.46), residues: 109 loop : -3.03 (0.21), residues: 768 *********************** 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 125 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 118 average time/residue: 0.2787 time to fit residues: 49.8007 Evaluate side-chains 99 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 1.599 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1387 time to fit residues: 4.5740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.6980 chunk 161 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 0.0470 overall best weight: 0.7280 ------------------------------------------------------------------------------- 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 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: 0.8206 moved from start: 0.3244 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= 0.167 Angle : 0.569 11.270 21226 Z= 0.285 Chirality : 0.037 0.161 2403 Planarity : 0.003 0.044 2618 Dihedral : 6.666 112.719 2238 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 0.83 % Allowed : 16.61 % Favored : 82.56 % 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: -1.21 (0.20), residues: 1817 helix: 0.92 (0.18), residues: 934 sheet: -1.65 (0.50), residues: 99 loop : -2.99 (0.21), residues: 784 *********************** 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 112 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 2.057 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 109 average time/residue: 0.2809 time to fit residues: 48.0453 Evaluate side-chains 98 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 1.647 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1799 time to fit residues: 4.3390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1407 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3369 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= 0.178 Angle : 0.570 10.759 21226 Z= 0.285 Chirality : 0.037 0.155 2403 Planarity : 0.003 0.046 2618 Dihedral : 6.602 112.968 2238 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 0.42 % Allowed : 17.56 % 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: -1.14 (0.20), residues: 1817 helix: 0.98 (0.18), residues: 939 sheet: -1.95 (0.48), residues: 109 loop : -2.94 (0.21), residues: 769 *********************** 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 105 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 1.917 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 103 average time/residue: 0.2787 time to fit residues: 45.1508 Evaluate side-chains 94 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 1.784 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1405 time to fit residues: 3.5445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.0980 chunk 106 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 121 optimal weight: 0.0470 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15658 Z= 0.137 Angle : 0.558 11.782 21226 Z= 0.277 Chirality : 0.037 0.163 2403 Planarity : 0.003 0.047 2618 Dihedral : 6.424 112.633 2238 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 0.18 % Allowed : 18.15 % Favored : 81.67 % 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: -0.94 (0.21), residues: 1817 helix: 1.13 (0.18), residues: 943 sheet: -1.81 (0.48), residues: 109 loop : -2.84 (0.21), residues: 765 *********************** 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 106 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 2.055 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 105 average time/residue: 0.2701 time to fit residues: 44.4335 Evaluate side-chains 94 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 1.850 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1430 time to fit residues: 3.1344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 100 optimal weight: 0.0000 chunk 72 optimal weight: 0.0770 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.2148 ------------------------------------------------------------------------------- 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: 0.8221 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15658 Z= 0.224 Angle : 0.609 11.006 21226 Z= 0.305 Chirality : 0.038 0.147 2403 Planarity : 0.003 0.048 2618 Dihedral : 6.561 113.245 2238 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 0.53 % Allowed : 18.33 % Favored : 81.14 % 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: -1.04 (0.20), residues: 1817 helix: 1.01 (0.18), residues: 946 sheet: -1.79 (0.48), residues: 109 loop : -2.85 (0.21), residues: 762 *********************** 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 102 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 1.710 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 100 average time/residue: 0.2660 time to fit residues: 42.9323 Evaluate side-chains 94 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 1.844 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1706 time to fit residues: 3.7233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 20.0000 chunk 107 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 169 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8188 moved from start: 0.3754 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= 0.169 Angle : 0.588 11.966 21226 Z= 0.291 Chirality : 0.037 0.189 2403 Planarity : 0.003 0.047 2618 Dihedral : 6.475 113.245 2238 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.24 % Allowed : 18.27 % 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: -0.93 (0.20), residues: 1817 helix: 1.09 (0.18), residues: 945 sheet: -1.70 (0.48), residues: 109 loop : -2.79 (0.22), residues: 763 ********************** 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 101 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 1.770 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 100 average time/residue: 0.2656 time to fit residues: 42.5393 Evaluate side-chains 92 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 1.744 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1332 time to fit residues: 2.6160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 135 optimal weight: 0.0970 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 146 optimal weight: 0.0000 chunk 61 optimal weight: 0.0870 chunk 150 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 overall best weight: 0.3560 ------------------------------------------------------------------------------- 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 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.081742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.057295 restraints weight = 63706.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.058956 restraints weight = 33799.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.059985 restraints weight = 22631.344| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3833 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= 0.142 Angle : 0.590 12.357 21226 Z= 0.290 Chirality : 0.037 0.221 2403 Planarity : 0.003 0.046 2618 Dihedral : 6.362 112.718 2238 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 0.24 % Allowed : 18.56 % 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: -0.83 (0.21), residues: 1817 helix: 1.16 (0.18), residues: 945 sheet: -1.64 (0.48), residues: 109 loop : -2.72 (0.22), residues: 763 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2821.31 seconds wall clock time: 53 minutes 1.58 seconds (3181.58 seconds total)