Starting phenix.real_space_refine on Sat Mar 16 10:00:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t02_25577/03_2024/7t02_25577_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t02_25577/03_2024/7t02_25577.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t02_25577/03_2024/7t02_25577_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t02_25577/03_2024/7t02_25577_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t02_25577/03_2024/7t02_25577_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t02_25577/03_2024/7t02_25577.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t02_25577/03_2024/7t02_25577.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t02_25577/03_2024/7t02_25577_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t02_25577/03_2024/7t02_25577_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 P 24 5.49 5 S 69 5.16 5 C 8955 2.51 5 N 2597 2.21 5 O 2709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 357": "OE1" <-> "OE2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A GLU 848": "OE1" <-> "OE2" Residue "A GLU 865": "OE1" <-> "OE2" Residue "A PHE 1820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1856": "OE1" <-> "OE2" Residue "A GLU 2077": "OE1" <-> "OE2" Residue "A GLU 2305": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14359 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1752, 13843 Classifications: {'peptide': 1752} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 79, 'TRANS': 1672} Chain breaks: 21 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 261 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' ZN': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3783 SG CYS A 817 67.269 68.841 59.841 1.00 19.31 S ATOM 3798 SG CYS A 819 64.678 66.345 59.573 1.00 21.74 S ATOM 3952 SG CYS A 840 64.904 68.631 62.673 1.00 21.58 S ATOM 3973 SG CYS A 843 67.375 65.782 62.299 1.00 22.56 S ATOM 6613 SG CYS A1200 40.256 38.972 29.021 1.00 59.05 S ATOM 7154 SG CYS A1271 40.631 35.766 31.022 1.00 58.67 S ATOM 7180 SG CYS A1274 42.883 38.798 31.636 1.00 51.12 S ATOM 3888 SG CYS A 832 74.619 80.216 62.537 1.00 26.03 S ATOM 3912 SG CYS A 835 77.726 79.986 60.191 1.00 27.37 S ATOM 5739 SG CYS A1065 79.129 79.281 63.034 1.00 24.90 S ATOM 12151 SG CYS A2081 84.350 78.363 87.720 1.00 67.71 S ATOM 12313 SG CYS A2104 81.125 79.742 86.428 1.00 67.93 S ATOM 12338 SG CYS A2107 84.246 77.826 84.239 1.00 63.42 S ATOM 12281 SG CYS A2099 82.084 64.922 87.906 1.00 37.84 S ATOM 12413 SG CYS A2117 84.893 66.132 86.436 1.00 40.58 S ATOM 12450 SG CYS A2123 86.160 63.935 86.507 1.00 38.16 S Time building chain proxies: 8.02, per 1000 atoms: 0.56 Number of scatterers: 14359 At special positions: 0 Unit cell: (117.04, 105.336, 123.424, 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 5 29.99 S 69 16.00 P 24 15.00 O 2709 8.00 N 2597 7.00 C 8955 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: 5.90 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2401 " pdb="ZN ZN A2401 " - pdb=" SG CYS A 817 " pdb="ZN ZN A2401 " - pdb=" SG CYS A 840 " pdb="ZN ZN A2401 " - pdb=" SG CYS A 819 " pdb="ZN ZN A2401 " - pdb=" SG CYS A 843 " pdb=" ZN A2402 " pdb="ZN ZN A2402 " - pdb=" ND1 HIS A1348 " pdb="ZN ZN A2402 " - pdb=" SG CYS A1274 " pdb="ZN ZN A2402 " - pdb=" SG CYS A1271 " pdb="ZN ZN A2402 " - pdb=" SG CYS A1200 " pdb=" ZN A2403 " pdb="ZN ZN A2403 " - pdb=" ND1 HIS A 849 " pdb="ZN ZN A2403 " - pdb=" SG CYS A 835 " pdb="ZN ZN A2403 " - pdb=" SG CYS A 832 " pdb="ZN ZN A2403 " - pdb=" SG CYS A1065 " pdb=" ZN A2404 " pdb="ZN ZN A2404 " - pdb=" SG CYS A2081 " pdb="ZN ZN A2404 " - pdb=" SG CYS A2107 " pdb="ZN ZN A2404 " - pdb=" SG CYS A2104 " pdb="ZN ZN A2404 " - pdb=" ND1 HIS A2083 " pdb=" ZN A2405 " pdb="ZN ZN A2405 " - pdb=" SG CYS A2123 " pdb="ZN ZN A2405 " - pdb=" SG CYS A2099 " pdb="ZN ZN A2405 " - pdb=" SG CYS A2117 " pdb="ZN ZN A2405 " - pdb=" ND1 HIS A2101 " Number of angles added : 18 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3332 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 18 sheets defined 37.0% alpha, 9.8% beta 2 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 7.78 Creating SS restraints... Processing helix chain 'A' and resid 321 through 329 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 358 through 374 Processing helix chain 'A' and resid 390 through 399 Processing helix chain 'A' and resid 410 through 413 removed outlier: 3.651A pdb=" N GLY A 413 " --> pdb=" O THR A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 413' Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 488 through 497 removed outlier: 3.688A pdb=" N GLN A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'A' and resid 535 through 545 Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 564 through 579 removed outlier: 4.182A pdb=" N LEU A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 603 removed outlier: 4.135A pdb=" N ARG A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 632 No H-bonds generated for 'chain 'A' and resid 629 through 632' Processing helix chain 'A' and resid 637 through 653 removed outlier: 4.297A pdb=" N ASP A 653 " --> pdb=" O ARG A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 708 Processing helix chain 'A' and resid 723 through 732 Processing helix chain 'A' and resid 736 through 749 Processing helix chain 'A' and resid 751 through 753 No H-bonds generated for 'chain 'A' and resid 751 through 753' Processing helix chain 'A' and resid 760 through 781 Processing helix chain 'A' and resid 803 through 813 removed outlier: 3.562A pdb=" N ARG A 812 " --> pdb=" O ASP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 883 through 895 Processing helix chain 'A' and resid 903 through 917 Processing helix chain 'A' and resid 970 through 974 Processing helix chain 'A' and resid 1020 through 1024 Processing helix chain 'A' and resid 1045 through 1050 Processing helix chain 'A' and resid 1190 through 1194 Processing helix chain 'A' and resid 1232 through 1239 removed outlier: 7.224A pdb=" N ASN A1237 " --> pdb=" O SER A1233 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N THR A1238 " --> pdb=" O HIS A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1249 removed outlier: 5.146A pdb=" N ARG A1249 " --> pdb=" O TRP A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1307 through 1318 Processing helix chain 'A' and resid 1344 through 1353 Processing helix chain 'A' and resid 1408 through 1421 removed outlier: 3.800A pdb=" N LEU A1413 " --> pdb=" O GLN A1409 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TRP A1414 " --> pdb=" O LEU A1410 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP A1415 " --> pdb=" O ARG A1411 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET A1416 " --> pdb=" O SER A1412 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A1418 " --> pdb=" O TRP A1414 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN A1419 " --> pdb=" O TRP A1415 " (cutoff:3.500A) Processing helix chain 'A' and resid 1473 through 1480 removed outlier: 4.126A pdb=" N ALA A1478 " --> pdb=" O ILE A1474 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N GLN A1479 " --> pdb=" O ALA A1475 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1518 removed outlier: 3.632A pdb=" N TRP A1511 " --> pdb=" O SER A1508 " (cutoff:3.500A) Proline residue: A1512 - end of helix Processing helix chain 'A' and resid 1539 through 1542 No H-bonds generated for 'chain 'A' and resid 1539 through 1542' Processing helix chain 'A' and resid 1552 through 1556 removed outlier: 3.881A pdb=" N GLU A1556 " --> pdb=" O SER A1552 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1552 through 1556' Processing helix chain 'A' and resid 1558 through 1568 Processing helix chain 'A' and resid 1583 through 1600 removed outlier: 4.032A pdb=" N ASP A1589 " --> pdb=" O CYS A1585 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A1590 " --> pdb=" O ASP A1586 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A1591 " --> pdb=" O ARG A1587 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A1594 " --> pdb=" O ALA A1590 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A1596 " --> pdb=" O MET A1592 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER A1597 " --> pdb=" O GLU A1593 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A1598 " --> pdb=" O SER A1594 " (cutoff:3.500A) Processing helix chain 'A' and resid 1727 through 1729 No H-bonds generated for 'chain 'A' and resid 1727 through 1729' Processing helix chain 'A' and resid 1735 through 1740 Processing helix chain 'A' and resid 1758 through 1768 Processing helix chain 'A' and resid 1782 through 1790 removed outlier: 3.876A pdb=" N LYS A1790 " --> pdb=" O LYS A1786 " (cutoff:3.500A) Processing helix chain 'A' and resid 1794 through 1802 Processing helix chain 'A' and resid 1807 through 1824 Processing helix chain 'A' and resid 1848 through 1863 Processing helix chain 'A' and resid 1877 through 1889 removed outlier: 4.283A pdb=" N ARG A1882 " --> pdb=" O SER A1878 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ALA A1889 " --> pdb=" O ARG A1885 " (cutoff:3.500A) Processing helix chain 'A' and resid 1896 through 1905 Processing helix chain 'A' and resid 1924 through 1960 Processing helix chain 'A' and resid 1972 through 1981 Processing helix chain 'A' and resid 1990 through 2002 Processing helix chain 'A' and resid 2028 through 2067 Processing helix chain 'A' and resid 2070 through 2077 removed outlier: 4.171A pdb=" N VAL A2075 " --> pdb=" O ASP A2071 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A2076 " --> pdb=" O ALA A2072 " (cutoff:3.500A) Processing helix chain 'A' and resid 2105 through 2113 removed outlier: 3.959A pdb=" N LYS A2110 " --> pdb=" O LYS A2106 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA A2111 " --> pdb=" O CYS A2107 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2138 No H-bonds generated for 'chain 'A' and resid 2135 through 2138' Processing helix chain 'A' and resid 2151 through 2162 Processing helix chain 'A' and resid 2176 through 2188 Processing helix chain 'A' and resid 2203 through 2210 Processing helix chain 'A' and resid 2252 through 2266 removed outlier: 4.117A pdb=" N VAL A2266 " --> pdb=" O ALA A2262 " (cutoff:3.500A) Processing helix chain 'A' and resid 2286 through 2302 removed outlier: 3.843A pdb=" N GLU A2300 " --> pdb=" O THR A2296 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 478 through 482 removed outlier: 3.617A pdb=" N VAL A 521 " --> pdb=" O ASN A 482 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 663 through 665 Processing sheet with id= C, first strand: chain 'A' and resid 838 through 840 Processing sheet with id= D, first strand: chain 'A' and resid 876 through 879 Processing sheet with id= E, first strand: chain 'A' and resid 996 through 998 removed outlier: 3.879A pdb=" N TYR A 926 " --> pdb=" O VAL A 936 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU A 938 " --> pdb=" O PHE A 924 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N PHE A 924 " --> pdb=" O GLU A 938 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1004 through 1007 Processing sheet with id= G, first strand: chain 'A' and resid 1016 through 1018 Processing sheet with id= H, first strand: chain 'A' and resid 1038 through 1041 removed outlier: 3.515A pdb=" N GLN A1060 " --> pdb=" O LYS A1074 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1088 through 1092 removed outlier: 3.507A pdb=" N ASP A1092 " --> pdb=" O ARG A1103 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG A1103 " --> pdb=" O ASP A1092 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1181 through 1184 removed outlier: 6.534A pdb=" N ILE A1339 " --> pdb=" O LEU A1206 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER A1208 " --> pdb=" O PHE A1337 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE A1337 " --> pdb=" O SER A1208 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG A1210 " --> pdb=" O GLY A1335 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY A1335 " --> pdb=" O ARG A1210 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1363 through 1366 removed outlier: 3.637A pdb=" N GLU A1451 " --> pdb=" O SER A1364 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1369 through 1371 Processing sheet with id= M, first strand: chain 'A' and resid 1747 through 1750 removed outlier: 6.479A pdb=" N GLY A1459 " --> pdb=" O ILE A1748 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N SER A1750 " --> pdb=" O GLY A1459 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE A1461 " --> pdb=" O SER A1750 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 1499 through 1502 removed outlier: 6.633A pdb=" N ARG A1721 " --> pdb=" O LEU A1500 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N VAL A1502 " --> pdb=" O ARG A1721 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE A1723 " --> pdb=" O VAL A1502 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'A' and resid 1837 through 1844 removed outlier: 6.477A pdb=" N VAL A2275 " --> pdb=" O VAL A1838 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N HIS A1840 " --> pdb=" O VAL A2275 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE A2277 " --> pdb=" O HIS A1840 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N HIS A1842 " --> pdb=" O ILE A2277 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ARG A2279 " --> pdb=" O HIS A1842 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N PHE A1844 " --> pdb=" O ARG A2279 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A2281 " --> pdb=" O PHE A1844 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'A' and resid 2093 through 2095 Processing sheet with id= Q, first strand: chain 'A' and resid 2241 through 2243 removed outlier: 6.520A pdb=" N LEU A2170 " --> pdb=" O VAL A2242 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A2221 " --> pdb=" O VAL A2169 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A2171 " --> pdb=" O LEU A2221 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 347 through 352 removed outlier: 3.542A pdb=" N VAL A 349 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N THR A 351 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER A 385 " --> pdb=" O THR A 351 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4 hydrogen bonds 8 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 5.80 Time building geometry restraints manager: 6.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2362 1.31 - 1.44: 3906 1.44 - 1.57: 8269 1.57 - 1.70: 50 1.70 - 1.82: 98 Bond restraints: 14685 Sorted by residual: bond pdb=" C2' 5CM B 30 " pdb=" C1' 5CM B 30 " ideal model delta sigma weight residual 1.521 1.307 0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C3' 5CM B 30 " pdb=" C2' 5CM B 30 " ideal model delta sigma weight residual 1.323 1.511 -0.188 2.00e-02 2.50e+03 8.79e+01 bond pdb=" C3' 5CM B 30 " pdb=" O3' 5CM B 30 " ideal model delta sigma weight residual 1.460 1.327 0.133 2.00e-02 2.50e+03 4.45e+01 bond pdb=" C1' 5CM B 30 " pdb=" N1 5CM B 30 " ideal model delta sigma weight residual 1.321 1.409 -0.088 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C5 5CM B 30 " pdb=" C5A 5CM B 30 " ideal model delta sigma weight residual 1.583 1.511 0.072 2.00e-02 2.50e+03 1.30e+01 ... (remaining 14680 not shown) Histogram of bond angle deviations from ideal: 97.97 - 105.38: 382 105.38 - 112.80: 8113 112.80 - 120.22: 5612 120.22 - 127.64: 5646 127.64 - 135.06: 215 Bond angle restraints: 19968 Sorted by residual: angle pdb=" C GLN A1731 " pdb=" N LYS A1732 " pdb=" CA LYS A1732 " ideal model delta sigma weight residual 121.54 131.75 -10.21 1.91e+00 2.74e-01 2.86e+01 angle pdb=" C GLN A1332 " pdb=" N ASP A1333 " pdb=" CA ASP A1333 " ideal model delta sigma weight residual 121.54 130.29 -8.75 1.91e+00 2.74e-01 2.10e+01 angle pdb=" C ILE A 388 " pdb=" N GLU A 389 " pdb=" CA GLU A 389 " ideal model delta sigma weight residual 121.98 111.04 10.94 3.11e+00 1.03e-01 1.24e+01 angle pdb=" C LEU A2283 " pdb=" N ASP A2284 " pdb=" CA ASP A2284 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 angle pdb=" CA PRO A2011 " pdb=" C PRO A2011 " pdb=" N PRO A2012 " ideal model delta sigma weight residual 117.93 122.11 -4.18 1.20e+00 6.94e-01 1.21e+01 ... (remaining 19963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 7771 17.80 - 35.59: 816 35.59 - 53.39: 193 53.39 - 71.19: 59 71.19 - 88.98: 22 Dihedral angle restraints: 8861 sinusoidal: 3772 harmonic: 5089 Sorted by residual: dihedral pdb=" CA GLN A2124 " pdb=" C GLN A2124 " pdb=" N ALA A2125 " pdb=" CA ALA A2125 " ideal model delta harmonic sigma weight residual -180.00 -152.41 -27.59 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA HIS A 849 " pdb=" C HIS A 849 " pdb=" N VAL A 850 " pdb=" CA VAL A 850 " ideal model delta harmonic sigma weight residual 180.00 153.85 26.15 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA MET A 734 " pdb=" C MET A 734 " pdb=" N THR A 735 " pdb=" CA THR A 735 " ideal model delta harmonic sigma weight residual -180.00 -154.47 -25.53 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 8858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1767 0.063 - 0.126: 404 0.126 - 0.188: 61 0.188 - 0.251: 9 0.251 - 0.314: 2 Chirality restraints: 2243 Sorted by residual: chirality pdb=" CB ILE A 332 " pdb=" CA ILE A 332 " pdb=" CG1 ILE A 332 " pdb=" CG2 ILE A 332 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CB ILE A 952 " pdb=" CA ILE A 952 " pdb=" CG1 ILE A 952 " pdb=" CG2 ILE A 952 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB ILE A 477 " pdb=" CA ILE A 477 " pdb=" CG1 ILE A 477 " pdb=" CG2 ILE A 477 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 2240 not shown) Planarity restraints: 2483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A2304 " 0.025 2.00e-02 2.50e+03 2.41e-02 1.45e+01 pdb=" CG TRP A2304 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A2304 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A2304 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A2304 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A2304 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A2304 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2304 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2304 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A2304 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A2284 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C ASP A2284 " -0.062 2.00e-02 2.50e+03 pdb=" O ASP A2284 " 0.024 2.00e-02 2.50e+03 pdb=" N THR A2285 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A1332 " 0.015 2.00e-02 2.50e+03 3.10e-02 9.62e+00 pdb=" C GLN A1332 " -0.054 2.00e-02 2.50e+03 pdb=" O GLN A1332 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP A1333 " 0.018 2.00e-02 2.50e+03 ... (remaining 2480 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 164 2.59 - 3.16: 12447 3.16 - 3.74: 21393 3.74 - 4.32: 28633 4.32 - 4.90: 47460 Nonbonded interactions: 110097 Sorted by model distance: nonbonded pdb=" O GLU A 834 " pdb="ZN ZN A2403 " model vdw 2.007 2.230 nonbonded pdb=" O GLU A 834 " pdb=" SG CYS A 835 " model vdw 2.211 3.400 nonbonded pdb=" O SER A1071 " pdb=" OG SER A1071 " model vdw 2.246 2.440 nonbonded pdb=" NH2 ARG A1802 " pdb=" OE1 GLU A1803 " model vdw 2.247 2.520 nonbonded pdb=" NH1 ARG A 398 " pdb=" O LEU A 717 " model vdw 2.256 2.520 ... (remaining 110092 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: 1.090 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: 4.530 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 47.760 Find NCS groups from input model: 0.380 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 : 0.010 0.214 14685 Z= 0.681 Angle : 0.993 10.936 19968 Z= 0.544 Chirality : 0.055 0.314 2243 Planarity : 0.006 0.070 2483 Dihedral : 16.502 88.983 5529 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 0.27 % Allowed : 0.53 % Favored : 99.20 % 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: -1.67 (0.19), residues: 1708 helix: 0.12 (0.19), residues: 698 sheet: -1.15 (0.31), residues: 277 loop : -2.32 (0.19), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP A2304 HIS 0.010 0.002 HIS A 849 PHE 0.031 0.003 PHE A1106 TYR 0.034 0.003 TYR A 851 ARG 0.010 0.001 ARG A 858 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 1.499 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.8869 (mtt) cc_final: 0.8533 (mtt) REVERT: A 1125 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8818 (tt) REVERT: A 1240 PHE cc_start: 0.7597 (m-80) cc_final: 0.7349 (m-80) REVERT: A 1975 GLU cc_start: 0.7475 (mp0) cc_final: 0.7210 (mp0) outliers start: 4 outliers final: 2 residues processed: 109 average time/residue: 0.2565 time to fit residues: 42.6633 Evaluate side-chains 80 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 696 ARG Chi-restraints excluded: chain A residue 1125 LEU Chi-restraints excluded: chain A residue 1253 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.7980 chunk 134 optimal weight: 0.9990 chunk 74 optimal weight: 0.0770 chunk 45 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1828 ASN A2254 ASN ** A2272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14685 Z= 0.196 Angle : 0.612 12.090 19968 Z= 0.317 Chirality : 0.040 0.215 2243 Planarity : 0.005 0.059 2483 Dihedral : 13.502 87.751 2151 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.80 % Allowed : 7.15 % Favored : 92.05 % 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: -0.86 (0.20), residues: 1708 helix: 0.93 (0.20), residues: 688 sheet: -0.87 (0.32), residues: 264 loop : -1.92 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1511 HIS 0.019 0.001 HIS A1373 PHE 0.021 0.001 PHE A1767 TYR 0.011 0.001 TYR A 513 ARG 0.004 0.000 ARG A1970 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 1.658 Fit side-chains REVERT: A 1240 PHE cc_start: 0.7586 (m-80) cc_final: 0.7373 (m-80) REVERT: A 1304 PHE cc_start: 0.6494 (m-80) cc_final: 0.6292 (m-80) REVERT: A 1332 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7905 (tm-30) REVERT: A 1975 GLU cc_start: 0.7358 (mp0) cc_final: 0.7024 (mp0) REVERT: A 2248 PHE cc_start: 0.7665 (p90) cc_final: 0.7367 (p90) outliers start: 12 outliers final: 5 residues processed: 115 average time/residue: 0.2395 time to fit residues: 43.9915 Evaluate side-chains 88 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 1259 TRP Chi-restraints excluded: chain A residue 2177 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 133 optimal weight: 0.0470 chunk 109 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1049 ASN ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2254 ASN ** A2278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 14685 Z= 0.321 Angle : 0.638 13.339 19968 Z= 0.327 Chirality : 0.041 0.199 2243 Planarity : 0.005 0.065 2483 Dihedral : 13.448 89.659 2143 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 1.27 % Allowed : 12.17 % Favored : 86.56 % 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: -0.77 (0.20), residues: 1708 helix: 1.05 (0.20), residues: 694 sheet: -0.86 (0.32), residues: 264 loop : -1.92 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1511 HIS 0.015 0.001 HIS A1373 PHE 0.018 0.002 PHE A1767 TYR 0.017 0.002 TYR A 522 ARG 0.005 0.000 ARG A 601 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 1.636 Fit side-chains REVERT: A 594 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7651 (tm-30) REVERT: A 1113 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8392 (pp) REVERT: A 1240 PHE cc_start: 0.7489 (m-80) cc_final: 0.7230 (m-80) REVERT: A 2248 PHE cc_start: 0.7787 (p90) cc_final: 0.7506 (p90) outliers start: 19 outliers final: 12 residues processed: 101 average time/residue: 0.2320 time to fit residues: 37.8095 Evaluate side-chains 93 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1259 TRP Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1855 LEU Chi-restraints excluded: chain A residue 2177 ASP Chi-restraints excluded: chain A residue 2296 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 83 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14685 Z= 0.317 Angle : 0.623 14.460 19968 Z= 0.319 Chirality : 0.041 0.195 2243 Planarity : 0.005 0.067 2483 Dihedral : 13.409 89.205 2143 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.27 % Allowed : 14.04 % Favored : 83.69 % 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: -0.73 (0.20), residues: 1708 helix: 1.12 (0.20), residues: 694 sheet: -0.88 (0.33), residues: 260 loop : -1.91 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1511 HIS 0.014 0.001 HIS A1373 PHE 0.018 0.002 PHE A1767 TYR 0.024 0.002 TYR A 522 ARG 0.004 0.000 ARG A 858 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 89 time to evaluate : 2.164 Fit side-chains REVERT: A 1113 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8413 (pp) REVERT: A 1240 PHE cc_start: 0.7528 (m-80) cc_final: 0.7320 (m-80) REVERT: A 2153 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7607 (mt) REVERT: A 2248 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.7603 (p90) outliers start: 34 outliers final: 18 residues processed: 113 average time/residue: 0.2479 time to fit residues: 45.6297 Evaluate side-chains 101 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1259 TRP Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1748 ILE Chi-restraints excluded: chain A residue 1855 LEU Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2153 LEU Chi-restraints excluded: chain A residue 2177 ASP Chi-restraints excluded: chain A residue 2248 PHE Chi-restraints excluded: chain A residue 2296 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14685 Z= 0.277 Angle : 0.603 15.036 19968 Z= 0.307 Chirality : 0.040 0.193 2243 Planarity : 0.005 0.058 2483 Dihedral : 13.347 89.854 2143 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.87 % Allowed : 15.24 % Favored : 81.89 % 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: -0.61 (0.20), residues: 1708 helix: 1.29 (0.21), residues: 687 sheet: -0.83 (0.33), residues: 267 loop : -1.90 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1511 HIS 0.013 0.001 HIS A1373 PHE 0.016 0.002 PHE A1767 TYR 0.024 0.002 TYR A 522 ARG 0.003 0.000 ARG A 858 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 91 time to evaluate : 1.765 Fit side-chains REVERT: A 1113 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8346 (pp) REVERT: A 1971 GLN cc_start: 0.7366 (mt0) cc_final: 0.6640 (mt0) REVERT: A 2153 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7553 (mt) outliers start: 43 outliers final: 28 residues processed: 123 average time/residue: 0.2199 time to fit residues: 43.9751 Evaluate side-chains 113 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 83 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1259 TRP Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1748 ILE Chi-restraints excluded: chain A residue 1855 LEU Chi-restraints excluded: chain A residue 1967 ASP Chi-restraints excluded: chain A residue 2090 ASP Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2153 LEU Chi-restraints excluded: chain A residue 2173 LEU Chi-restraints excluded: chain A residue 2177 ASP Chi-restraints excluded: chain A residue 2289 THR Chi-restraints excluded: chain A residue 2296 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 171 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14685 Z= 0.358 Angle : 0.646 15.597 19968 Z= 0.329 Chirality : 0.042 0.198 2243 Planarity : 0.005 0.059 2483 Dihedral : 13.445 88.370 2143 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.94 % Allowed : 15.98 % Favored : 80.08 % 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: -0.68 (0.20), residues: 1708 helix: 1.23 (0.21), residues: 682 sheet: -0.88 (0.33), residues: 261 loop : -1.90 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1511 HIS 0.012 0.001 HIS A1373 PHE 0.015 0.002 PHE A1767 TYR 0.031 0.002 TYR A 522 ARG 0.004 0.000 ARG A 601 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 87 time to evaluate : 1.595 Fit side-chains REVERT: A 1113 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8411 (pp) REVERT: A 1971 GLN cc_start: 0.7290 (mt0) cc_final: 0.6651 (mt0) REVERT: A 2153 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7529 (mt) outliers start: 59 outliers final: 38 residues processed: 134 average time/residue: 0.2249 time to fit residues: 48.6873 Evaluate side-chains 124 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 84 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1155 LEU Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1259 TRP Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1602 LEU Chi-restraints excluded: chain A residue 1748 ILE Chi-restraints excluded: chain A residue 1866 MET Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1967 ASP Chi-restraints excluded: chain A residue 2081 CYS Chi-restraints excluded: chain A residue 2090 ASP Chi-restraints excluded: chain A residue 2144 LEU Chi-restraints excluded: chain A residue 2153 LEU Chi-restraints excluded: chain A residue 2173 LEU Chi-restraints excluded: chain A residue 2177 ASP Chi-restraints excluded: chain A residue 2223 LEU Chi-restraints excluded: chain A residue 2285 THR Chi-restraints excluded: chain A residue 2289 THR Chi-restraints excluded: chain A residue 2296 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 106 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1373 HIS ** A1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1927 HIS ** A2278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14685 Z= 0.226 Angle : 0.580 15.179 19968 Z= 0.294 Chirality : 0.039 0.192 2243 Planarity : 0.004 0.061 2483 Dihedral : 13.220 88.265 2143 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.21 % Allowed : 17.58 % Favored : 79.21 % 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: -0.43 (0.21), residues: 1708 helix: 1.50 (0.21), residues: 674 sheet: -0.76 (0.33), residues: 268 loop : -1.79 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1511 HIS 0.011 0.001 HIS A1373 PHE 0.014 0.001 PHE A1767 TYR 0.024 0.002 TYR A 522 ARG 0.004 0.000 ARG A 398 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 99 time to evaluate : 1.650 Fit side-chains REVERT: A 923 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7882 (mtt180) REVERT: A 1113 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8317 (pp) REVERT: A 1971 GLN cc_start: 0.7243 (mt0) cc_final: 0.6632 (mt0) REVERT: A 2153 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7525 (mt) REVERT: A 2304 TRP cc_start: 0.5835 (OUTLIER) cc_final: 0.5219 (p90) outliers start: 48 outliers final: 31 residues processed: 138 average time/residue: 0.2349 time to fit residues: 51.9470 Evaluate side-chains 121 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 86 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 923 ARG Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1253 LEU Chi-restraints excluded: chain A residue 1259 TRP Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1748 ILE Chi-restraints excluded: chain A residue 1752 THR Chi-restraints excluded: chain A residue 1791 ASP Chi-restraints excluded: chain A residue 1838 VAL Chi-restraints excluded: chain A residue 1967 ASP Chi-restraints excluded: chain A residue 2081 CYS Chi-restraints excluded: chain A residue 2090 ASP Chi-restraints excluded: chain A residue 2153 LEU Chi-restraints excluded: chain A residue 2173 LEU Chi-restraints excluded: chain A residue 2177 ASP Chi-restraints excluded: chain A residue 2223 LEU Chi-restraints excluded: chain A residue 2285 THR Chi-restraints excluded: chain A residue 2289 THR Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 51 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1715 HIS ** A1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14685 Z= 0.188 Angle : 0.565 15.215 19968 Z= 0.285 Chirality : 0.039 0.187 2243 Planarity : 0.004 0.064 2483 Dihedral : 13.046 85.834 2143 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.61 % Allowed : 18.65 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1708 helix: 1.70 (0.21), residues: 671 sheet: -0.67 (0.33), residues: 263 loop : -1.69 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1511 HIS 0.005 0.001 HIS A 849 PHE 0.017 0.001 PHE A1584 TYR 0.019 0.001 TYR A 522 ARG 0.003 0.000 ARG A 398 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 100 time to evaluate : 1.567 Fit side-chains REVERT: A 923 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7845 (mtt180) REVERT: A 1113 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8230 (pp) REVERT: A 1971 GLN cc_start: 0.7234 (mt0) cc_final: 0.6250 (mt0) REVERT: A 1975 GLU cc_start: 0.7453 (mp0) cc_final: 0.7172 (mp0) REVERT: A 2304 TRP cc_start: 0.5713 (OUTLIER) cc_final: 0.5140 (p90) outliers start: 39 outliers final: 30 residues processed: 127 average time/residue: 0.2253 time to fit residues: 45.1909 Evaluate side-chains 120 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 87 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 923 ARG Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1259 TRP Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1732 LYS Chi-restraints excluded: chain A residue 1748 ILE Chi-restraints excluded: chain A residue 1752 THR Chi-restraints excluded: chain A residue 1838 VAL Chi-restraints excluded: chain A residue 1967 ASP Chi-restraints excluded: chain A residue 2081 CYS Chi-restraints excluded: chain A residue 2173 LEU Chi-restraints excluded: chain A residue 2177 ASP Chi-restraints excluded: chain A residue 2223 LEU Chi-restraints excluded: chain A residue 2285 THR Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 chunk 158 optimal weight: 0.0060 chunk 95 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 124 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 overall best weight: 1.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14685 Z= 0.224 Angle : 0.586 15.910 19968 Z= 0.292 Chirality : 0.039 0.187 2243 Planarity : 0.004 0.064 2483 Dihedral : 13.053 87.222 2143 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.81 % Allowed : 18.72 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.21), residues: 1708 helix: 1.66 (0.21), residues: 677 sheet: -0.66 (0.33), residues: 263 loop : -1.71 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A1511 HIS 0.006 0.001 HIS A 849 PHE 0.013 0.001 PHE A2248 TYR 0.022 0.001 TYR A 522 ARG 0.004 0.000 ARG A 398 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 94 time to evaluate : 1.761 Fit side-chains REVERT: A 923 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7827 (mtt180) REVERT: A 1113 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8341 (pp) REVERT: A 1240 PHE cc_start: 0.7321 (m-80) cc_final: 0.7078 (m-80) REVERT: A 1897 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6945 (tm-30) REVERT: A 1911 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8315 (mm) REVERT: A 1971 GLN cc_start: 0.7205 (mt0) cc_final: 0.6580 (mt0) REVERT: A 2304 TRP cc_start: 0.5737 (OUTLIER) cc_final: 0.5171 (p90) outliers start: 42 outliers final: 33 residues processed: 125 average time/residue: 0.2512 time to fit residues: 49.1850 Evaluate side-chains 125 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 88 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 923 ARG Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1259 TRP Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1732 LYS Chi-restraints excluded: chain A residue 1748 ILE Chi-restraints excluded: chain A residue 1752 THR Chi-restraints excluded: chain A residue 1838 VAL Chi-restraints excluded: chain A residue 1911 LEU Chi-restraints excluded: chain A residue 1967 ASP Chi-restraints excluded: chain A residue 2081 CYS Chi-restraints excluded: chain A residue 2173 LEU Chi-restraints excluded: chain A residue 2177 ASP Chi-restraints excluded: chain A residue 2223 LEU Chi-restraints excluded: chain A residue 2285 THR Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14685 Z= 0.187 Angle : 0.572 15.783 19968 Z= 0.285 Chirality : 0.039 0.188 2243 Planarity : 0.004 0.064 2483 Dihedral : 12.945 85.741 2143 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.41 % Allowed : 19.32 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.21), residues: 1708 helix: 1.76 (0.21), residues: 675 sheet: -0.66 (0.33), residues: 265 loop : -1.64 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1511 HIS 0.005 0.001 HIS A 849 PHE 0.012 0.001 PHE A 864 TYR 0.019 0.001 TYR A 522 ARG 0.003 0.000 ARG A 398 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 95 time to evaluate : 1.722 Fit side-chains REVERT: A 923 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7767 (mtt180) REVERT: A 1113 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8265 (pp) REVERT: A 1971 GLN cc_start: 0.7185 (mt0) cc_final: 0.6669 (mt0) REVERT: A 1975 GLU cc_start: 0.7441 (mp0) cc_final: 0.7138 (mp0) REVERT: A 2304 TRP cc_start: 0.5715 (OUTLIER) cc_final: 0.5116 (p90) outliers start: 36 outliers final: 32 residues processed: 122 average time/residue: 0.2421 time to fit residues: 46.6669 Evaluate side-chains 125 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 90 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 743 MET Chi-restraints excluded: chain A residue 923 ARG Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1259 TRP Chi-restraints excluded: chain A residue 1281 ILE Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1527 VAL Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1732 LYS Chi-restraints excluded: chain A residue 1748 ILE Chi-restraints excluded: chain A residue 1752 THR Chi-restraints excluded: chain A residue 1838 VAL Chi-restraints excluded: chain A residue 1967 ASP Chi-restraints excluded: chain A residue 2081 CYS Chi-restraints excluded: chain A residue 2173 LEU Chi-restraints excluded: chain A residue 2177 ASP Chi-restraints excluded: chain A residue 2223 LEU Chi-restraints excluded: chain A residue 2285 THR Chi-restraints excluded: chain A residue 2304 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 144 optimal weight: 0.0270 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 0.0970 chunk 123 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2278 HIS ** 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 = 0.3866 r_free = 0.3866 target = 0.141710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.119100 restraints weight = 23675.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119558 restraints weight = 22466.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.120651 restraints weight = 21016.119| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14685 Z= 0.141 Angle : 0.545 15.658 19968 Z= 0.271 Chirality : 0.038 0.182 2243 Planarity : 0.004 0.064 2483 Dihedral : 12.668 82.586 2143 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.87 % Allowed : 19.99 % Favored : 78.14 % 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: 0.12 (0.21), residues: 1708 helix: 1.94 (0.21), residues: 671 sheet: -0.45 (0.33), residues: 263 loop : -1.46 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A1511 HIS 0.005 0.001 HIS A 567 PHE 0.015 0.001 PHE A 864 TYR 0.012 0.001 TYR A1854 ARG 0.005 0.000 ARG A1445 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2195.71 seconds wall clock time: 40 minutes 56.57 seconds (2456.57 seconds total)