Starting phenix.real_space_refine on Sat Mar 16 18:42:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asb_15610/03_2024/8asb_15610_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asb_15610/03_2024/8asb_15610.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asb_15610/03_2024/8asb_15610_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asb_15610/03_2024/8asb_15610_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asb_15610/03_2024/8asb_15610_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asb_15610/03_2024/8asb_15610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asb_15610/03_2024/8asb_15610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asb_15610/03_2024/8asb_15610_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asb_15610/03_2024/8asb_15610_updated.pdb" } resolution = 3.6 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 873 atoms to isotropic. 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 P 40 5.49 5 Mg 1 5.21 5 S 82 5.16 5 C 9019 2.51 5 N 2529 2.21 5 O 2816 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 794": "OD1" <-> "OD2" Residue "A PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 831": "OE1" <-> "OE2" Residue "A PHE 854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1127": "OD1" <-> "OD2" Residue "A TYR 1309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1363": "OE1" <-> "OE2" Residue "A TYR 1373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1519": "OE1" <-> "OE2" Residue "A GLU 1823": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14487 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13649 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1715, 13628 Classifications: {'peptide': 1715} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 1651} Chain breaks: 10 Conformer: "B" Number of residues, atoms: 1715, 13628 Classifications: {'peptide': 1715} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 1651} Chain breaks: 10 bond proxies already assigned to first conformer: 13879 Chain: "P" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 363 Classifications: {'RNA': 17} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 13} Chain: "T" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 381 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 10} Link IDs: {'rna2p': 3, 'rna3p': 14} Chain: "G" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, '2KH': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.98, per 1000 atoms: 0.97 Number of scatterers: 14487 At special positions: 0 Unit cell: (115.6, 110.5, 126.65, 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) S 82 16.00 P 40 15.00 Mg 1 11.99 O 2816 8.00 N 2529 7.00 C 9019 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.10 Conformation dependent library (CDL) restraints added in 5.1 seconds 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3212 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 14 sheets defined 46.1% alpha, 7.5% beta 6 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 9.23 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 Processing helix chain 'A' and resid 75 through 82 removed outlier: 5.240A pdb=" N ASN A 79 " --> pdb=" O TYR A 76 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP A 81 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 98 No H-bonds generated for 'chain 'A' and resid 95 through 98' Processing helix chain 'A' and resid 136 through 159 removed outlier: 4.596A pdb=" N ASP A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Proline residue: A 152 - end of helix removed outlier: 4.447A pdb=" N ASP A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 207 removed outlier: 4.084A pdb=" N SER A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 212 No H-bonds generated for 'chain 'A' and resid 209 through 212' Processing helix chain 'A' and resid 218 through 232 Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 263 through 285 Processing helix chain 'A' and resid 293 through 317 Processing helix chain 'A' and resid 359 through 374 removed outlier: 3.844A pdb=" N ASP A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 391 removed outlier: 3.729A pdb=" N ILE A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.705A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 446 Processing helix chain 'A' and resid 457 through 464 Processing helix chain 'A' and resid 478 through 490 Processing helix chain 'A' and resid 492 through 494 No H-bonds generated for 'chain 'A' and resid 492 through 494' Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.699A pdb=" N TRP A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LYS A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 610 Processing helix chain 'A' and resid 612 through 625 Processing helix chain 'A' and resid 639 through 654 Processing helix chain 'A' and resid 657 through 674 removed outlier: 3.808A pdb=" N ILE A 662 " --> pdb=" O LYS A 658 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE A 663 " --> pdb=" O THR A 659 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 666 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ARG A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TYR A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLY A 673 " --> pdb=" O THR A 669 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N PHE A 674 " --> pdb=" O GLN A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 687 removed outlier: 3.714A pdb=" N MET A 686 " --> pdb=" O PRO A 683 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 687 " --> pdb=" O GLN A 684 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 683 through 687' Processing helix chain 'A' and resid 697 through 715 Processing helix chain 'A' and resid 743 through 755 removed outlier: 3.896A pdb=" N TYR A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLY A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TYR A 754 " --> pdb=" O TRP A 750 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TYR A 755 " --> pdb=" O TYR A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 776 removed outlier: 4.034A pdb=" N GLY A 768 " --> pdb=" O ASN A 765 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU A 769 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET A 770 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS A 773 " --> pdb=" O MET A 770 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 774 " --> pdb=" O TYR A 771 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU A 776 " --> pdb=" O LYS A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 787 No H-bonds generated for 'chain 'A' and resid 785 through 787' Processing helix chain 'A' and resid 803 through 821 Processing helix chain 'A' and resid 825 through 839 Processing helix chain 'A' and resid 843 through 845 No H-bonds generated for 'chain 'A' and resid 843 through 845' Processing helix chain 'A' and resid 856 through 858 No H-bonds generated for 'chain 'A' and resid 856 through 858' Processing helix chain 'A' and resid 874 through 883 Processing helix chain 'A' and resid 889 through 903 removed outlier: 3.869A pdb=" N VAL A 893 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLY A 894 " --> pdb=" O ASP A 891 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 901 " --> pdb=" O LYS A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 946 removed outlier: 3.905A pdb=" N LEU A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 946 " --> pdb=" O CYS A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 957 No H-bonds generated for 'chain 'A' and resid 955 through 957' Processing helix chain 'A' and resid 961 through 973 removed outlier: 4.038A pdb=" N GLY A 966 " --> pdb=" O ILE A 962 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 967 " --> pdb=" O GLU A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 992 No H-bonds generated for 'chain 'A' and resid 989 through 992' Processing helix chain 'A' and resid 997 through 1004 Processing helix chain 'A' and resid 1008 through 1022 removed outlier: 3.546A pdb=" N HIS A1011 " --> pdb=" O ALA A1008 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ARG A1012 " --> pdb=" O LYS A1009 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A1013 " --> pdb=" O PHE A1010 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N TRP A1015 " --> pdb=" O ARG A1012 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A1016 " --> pdb=" O PHE A1013 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A1018 " --> pdb=" O TRP A1015 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET A1020 " --> pdb=" O ALA A1017 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A1022 " --> pdb=" O SER A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1037 Processing helix chain 'A' and resid 1047 through 1056 Processing helix chain 'A' and resid 1084 through 1108 Processing helix chain 'A' and resid 1139 through 1154 removed outlier: 3.861A pdb=" N VAL A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG A1144 " --> pdb=" O MET A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1163 Proline residue: A1161 - end of helix Processing helix chain 'A' and resid 1195 through 1199 Processing helix chain 'A' and resid 1211 through 1227 removed outlier: 3.875A pdb=" N GLN A1215 " --> pdb=" O LEU A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1249 Processing helix chain 'A' and resid 1256 through 1267 removed outlier: 4.521A pdb=" N GLY A1259 " --> pdb=" O PRO A1256 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR A1260 " --> pdb=" O LEU A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1273 No H-bonds generated for 'chain 'A' and resid 1271 through 1273' Processing helix chain 'A' and resid 1281 through 1283 No H-bonds generated for 'chain 'A' and resid 1281 through 1283' Processing helix chain 'A' and resid 1289 through 1299 Processing helix chain 'A' and resid 1302 through 1312 Processing helix chain 'A' and resid 1343 through 1355 removed outlier: 6.116A pdb=" N LYS A1347 " --> pdb=" O ASP A1344 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR A1348 " --> pdb=" O ARG A1345 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN A1349 " --> pdb=" O LYS A1346 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG A1354 " --> pdb=" O LEU A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1367 Processing helix chain 'A' and resid 1369 through 1371 No H-bonds generated for 'chain 'A' and resid 1369 through 1371' Processing helix chain 'A' and resid 1379 through 1390 Processing helix chain 'A' and resid 1393 through 1398 removed outlier: 3.571A pdb=" N SER A1398 " --> pdb=" O GLY A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1411 removed outlier: 3.782A pdb=" N ALA A1411 " --> pdb=" O ARG A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1447 Processing helix chain 'A' and resid 1458 through 1464 Processing helix chain 'A' and resid 1468 through 1475 Processing helix chain 'A' and resid 1513 through 1522 Processing helix chain 'A' and resid 1531 through 1544 Processing helix chain 'A' and resid 1552 through 1557 Processing helix chain 'A' and resid 1564 through 1574 Processing helix chain 'A' and resid 1596 through 1604 Processing helix chain 'A' and resid 1670 through 1682 Processing helix chain 'A' and resid 1688 through 1694 Processing helix chain 'A' and resid 1758 through 1772 removed outlier: 3.604A pdb=" N ASP A1771 " --> pdb=" O ARG A1767 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A1772 " --> pdb=" O LEU A1768 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 22 through 25 Processing sheet with id= B, first strand: chain 'A' and resid 36 through 40 Processing sheet with id= C, first strand: chain 'A' and resid 410 through 412 removed outlier: 8.314A pdb=" N GLU A 540 " --> pdb=" O PRO A 557 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 569 through 571 Processing sheet with id= E, first strand: chain 'A' and resid 719 through 722 Processing sheet with id= F, first strand: chain 'A' and resid 921 through 925 removed outlier: 4.098A pdb=" N LEU A 910 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 978 through 984 Processing sheet with id= H, first strand: chain 'A' and resid 1178 through 1180 Processing sheet with id= I, first strand: chain 'A' and resid 1486 through 1488 Processing sheet with id= J, first strand: chain 'A' and resid 1496 through 1500 Processing sheet with id= K, first strand: chain 'A' and resid 1700 through 1703 Processing sheet with id= L, first strand: chain 'A' and resid 1738 through 1740 Processing sheet with id= M, first strand: chain 'A' and resid 1750 through 1752 removed outlier: 4.023A pdb=" N ILE A1750 " --> pdb=" O PRO A1805 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A1788 " --> pdb=" O VAL A1806 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG A1789 " --> pdb=" O LYS A1796 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A1794 " --> pdb=" O SER A1791 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 335 through 337 removed outlier: 3.540A pdb=" N ARG A 577 " --> pdb=" O LEU A 336 " (cutoff:3.500A) 538 hydrogen bonds defined for protein. 1473 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 6.55 Time building geometry restraints manager: 6.60 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: 2301 1.31 - 1.43: 4162 1.43 - 1.56: 8185 1.56 - 1.69: 76 1.69 - 1.81: 136 Bond restraints: 14860 Sorted by residual: bond pdb=" C3' 2KH A2102 " pdb=" C4' 2KH A2102 " ideal model delta sigma weight residual 1.643 1.297 0.346 2.00e-02 2.50e+03 2.99e+02 bond pdb=" C4' 2KH A2102 " pdb=" O4' 2KH A2102 " ideal model delta sigma weight residual 1.310 1.611 -0.301 2.00e-02 2.50e+03 2.27e+02 bond pdb=" C1' 2KH A2102 " pdb=" O4' 2KH A2102 " ideal model delta sigma weight residual 1.561 1.306 0.255 2.00e-02 2.50e+03 1.62e+02 bond pdb=" C2' 2KH A2102 " pdb=" C3' 2KH A2102 " ideal model delta sigma weight residual 1.312 1.534 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C1' 2KH A2102 " pdb=" N1 2KH A2102 " ideal model delta sigma weight residual 1.322 1.475 -0.153 2.00e-02 2.50e+03 5.89e+01 ... (remaining 14855 not shown) Histogram of bond angle deviations from ideal: 99.11 - 106.15: 510 106.15 - 113.18: 8082 113.18 - 120.22: 5384 120.22 - 127.26: 6042 127.26 - 134.29: 216 Bond angle restraints: 20234 Sorted by residual: angle pdb=" CA MET A1826 " pdb=" CB MET A1826 " pdb=" CG MET A1826 " ideal model delta sigma weight residual 114.10 122.59 -8.49 2.00e+00 2.50e-01 1.80e+01 angle pdb=" N ILE A 135 " pdb=" CA ILE A 135 " pdb=" C ILE A 135 " ideal model delta sigma weight residual 112.96 108.84 4.12 1.00e+00 1.00e+00 1.70e+01 angle pdb=" O3' G T 13 " pdb=" C3' G T 13 " pdb=" C2' G T 13 " ideal model delta sigma weight residual 113.70 118.84 -5.14 1.50e+00 4.44e-01 1.17e+01 angle pdb=" C PHE A 548 " pdb=" N TRP A 549 " pdb=" CA TRP A 549 " ideal model delta sigma weight residual 120.97 130.67 -9.70 2.84e+00 1.24e-01 1.17e+01 angle pdb=" CA ARG A1012 " pdb=" CB ARG A1012 " pdb=" CG ARG A1012 " ideal model delta sigma weight residual 114.10 120.50 -6.40 2.00e+00 2.50e-01 1.03e+01 ... (remaining 20229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.34: 8553 27.34 - 54.69: 398 54.69 - 82.03: 72 82.03 - 109.38: 7 109.38 - 136.72: 2 Dihedral angle restraints: 9032 sinusoidal: 4060 harmonic: 4972 Sorted by residual: dihedral pdb=" CA GLU A 126 " pdb=" C GLU A 126 " pdb=" N PHE A 127 " pdb=" CA PHE A 127 " ideal model delta harmonic sigma weight residual -180.00 -157.38 -22.62 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA THR A 995 " pdb=" C THR A 995 " pdb=" N THR A 996 " pdb=" CA THR A 996 " ideal model delta harmonic sigma weight residual 180.00 159.60 20.40 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" O1A 2KH A2102 " pdb=" N3A 2KH A2102 " pdb=" PA 2KH A2102 " pdb=" PB 2KH A2102 " ideal model delta sinusoidal sigma weight residual -34.41 -146.37 111.96 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 9029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1791 0.050 - 0.099: 372 0.099 - 0.149: 94 0.149 - 0.199: 8 0.199 - 0.249: 3 Chirality restraints: 2268 Sorted by residual: chirality pdb=" C3' G T 13 " pdb=" C4' G T 13 " pdb=" O3' G T 13 " pdb=" C2' G T 13 " both_signs ideal model delta sigma weight residual False -2.48 -2.23 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB ILE A 564 " pdb=" CA ILE A 564 " pdb=" CG1 ILE A 564 " pdb=" CG2 ILE A 564 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ASP A1268 " pdb=" N ASP A1268 " pdb=" C ASP A1268 " pdb=" CB ASP A1268 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 2265 not shown) Planarity restraints: 2438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 897 " -0.028 2.00e-02 2.50e+03 2.22e-02 1.24e+01 pdb=" CG TRP A 897 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP A 897 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 897 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 897 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 897 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 897 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 897 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 897 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 897 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 556 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.83e+00 pdb=" N PRO A 557 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 557 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 557 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A1712 " 0.036 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A1713 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A1713 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1713 " 0.031 5.00e-02 4.00e+02 ... (remaining 2435 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 296 2.68 - 3.24: 13564 3.24 - 3.79: 23274 3.79 - 4.35: 30435 4.35 - 4.90: 49057 Nonbonded interactions: 116626 Sorted by model distance: nonbonded pdb="MG MG A2101 " pdb=" O2A 2KH A2102 " model vdw 2.130 2.170 nonbonded pdb=" OD1 ASP A 985 " pdb="MG MG A2101 " model vdw 2.134 2.170 nonbonded pdb=" OH TYR A 286 " pdb=" OE1 GLU A 303 " model vdw 2.188 2.440 nonbonded pdb=" OG1 THR A 951 " pdb=" OH TYR A1181 " model vdw 2.222 2.440 nonbonded pdb=" OD2 ASP A1126 " pdb="MG MG A2101 " model vdw 2.226 2.170 ... (remaining 116621 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=0.31 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 7.190 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 57.860 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.080 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:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 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 : 0.006 0.346 14860 Z= 0.372 Angle : 0.682 9.704 20234 Z= 0.357 Chirality : 0.044 0.249 2268 Planarity : 0.005 0.060 2438 Dihedral : 15.533 136.722 5820 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.07 % Allowed : 0.13 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.19), residues: 1697 helix: 0.43 (0.18), residues: 791 sheet: -0.38 (0.43), residues: 148 loop : -1.83 (0.20), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP A 897 HIS 0.010 0.001 HIS A 916 PHE 0.037 0.002 PHE A 84 TYR 0.035 0.002 TYR A 202 ARG 0.013 0.001 ARG A1542 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 358 time to evaluate : 1.714 Fit side-chains REVERT: A 200 GLU cc_start: 0.7317 (tp30) cc_final: 0.6444 (tp30) REVERT: A 204 LYS cc_start: 0.7705 (mtmm) cc_final: 0.6986 (mtmm) REVERT: A 213 GLU cc_start: 0.6865 (mp0) cc_final: 0.6419 (mp0) REVERT: A 271 LYS cc_start: 0.7641 (ptpp) cc_final: 0.7095 (ptpp) REVERT: A 302 CYS cc_start: 0.7800 (t) cc_final: 0.7397 (t) REVERT: A 306 ASP cc_start: 0.7321 (m-30) cc_final: 0.6982 (m-30) REVERT: A 488 GLU cc_start: 0.7103 (tp30) cc_final: 0.6776 (tp30) REVERT: A 489 LYS cc_start: 0.7722 (ttmt) cc_final: 0.7440 (tttt) REVERT: A 495 ASP cc_start: 0.7373 (p0) cc_final: 0.7170 (p0) REVERT: A 618 ASN cc_start: 0.7334 (m-40) cc_final: 0.7017 (m-40) REVERT: A 661 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6585 (mm-30) REVERT: A 719 SER cc_start: 0.8394 (t) cc_final: 0.8109 (t) REVERT: A 759 GLU cc_start: 0.6815 (tp30) cc_final: 0.6492 (mm-30) REVERT: A 856 LYS cc_start: 0.7637 (tmtt) cc_final: 0.7405 (tmtt) REVERT: A 864 VAL cc_start: 0.8018 (m) cc_final: 0.7802 (p) REVERT: A 887 MET cc_start: 0.6732 (tmm) cc_final: 0.6177 (tmm) REVERT: A 964 ASN cc_start: 0.7780 (m-40) cc_final: 0.7556 (m-40) REVERT: A 1032 PHE cc_start: 0.7850 (t80) cc_final: 0.7555 (t80) REVERT: A 1064 TRP cc_start: 0.7426 (p-90) cc_final: 0.7171 (p-90) REVERT: A 1108 GLU cc_start: 0.7636 (pp20) cc_final: 0.7174 (pp20) REVERT: A 1123 GLU cc_start: 0.7027 (pp20) cc_final: 0.6588 (pp20) REVERT: A 1141 ASP cc_start: 0.7166 (t0) cc_final: 0.6722 (t0) REVERT: A 1182 ASN cc_start: 0.7904 (m-40) cc_final: 0.7698 (m-40) REVERT: A 1227 GLU cc_start: 0.7116 (pp20) cc_final: 0.6844 (pp20) REVERT: A 1610 SER cc_start: 0.8037 (m) cc_final: 0.7810 (m) REVERT: A 1845 MET cc_start: 0.5366 (ptm) cc_final: 0.4717 (ptm) outliers start: 1 outliers final: 1 residues processed: 358 average time/residue: 0.3402 time to fit residues: 166.8399 Evaluate side-chains 334 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 333 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 1.9990 chunk 131 optimal weight: 0.0770 chunk 72 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 ASN A1569 ASN A1604 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14860 Z= 0.230 Angle : 0.566 8.632 20234 Z= 0.291 Chirality : 0.041 0.174 2268 Planarity : 0.004 0.058 2438 Dihedral : 12.898 138.545 2466 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.60 % Allowed : 9.42 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.59 (0.20), residues: 1697 helix: 0.85 (0.18), residues: 800 sheet: -0.30 (0.43), residues: 148 loop : -1.83 (0.20), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 897 HIS 0.011 0.001 HIS A 916 PHE 0.025 0.002 PHE A1048 TYR 0.020 0.002 TYR A 754 ARG 0.011 0.001 ARG A1497 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 353 time to evaluate : 1.599 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6973 (ppp) cc_final: 0.6430 (pmm) REVERT: A 145 LYS cc_start: 0.7209 (mmtt) cc_final: 0.6965 (ttmm) REVERT: A 200 GLU cc_start: 0.7436 (tp30) cc_final: 0.6934 (tp30) REVERT: A 213 GLU cc_start: 0.6881 (mp0) cc_final: 0.6614 (mp0) REVERT: A 239 GLU cc_start: 0.7418 (pp20) cc_final: 0.7143 (pp20) REVERT: A 271 LYS cc_start: 0.7945 (ptpp) cc_final: 0.7397 (ptpp) REVERT: A 302 CYS cc_start: 0.7848 (t) cc_final: 0.7484 (t) REVERT: A 306 ASP cc_start: 0.7351 (m-30) cc_final: 0.7032 (m-30) REVERT: A 488 GLU cc_start: 0.7232 (tp30) cc_final: 0.6893 (tp30) REVERT: A 489 LYS cc_start: 0.7828 (ttmt) cc_final: 0.7439 (tttt) REVERT: A 495 ASP cc_start: 0.7499 (p0) cc_final: 0.7283 (p0) REVERT: A 655 ASP cc_start: 0.7202 (t70) cc_final: 0.6943 (t0) REVERT: A 661 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6640 (mm-30) REVERT: A 671 MET cc_start: 0.6699 (mmm) cc_final: 0.6432 (tpp) REVERT: A 719 SER cc_start: 0.8431 (t) cc_final: 0.8192 (t) REVERT: A 759 GLU cc_start: 0.6706 (tp30) cc_final: 0.6501 (mm-30) REVERT: A 856 LYS cc_start: 0.7688 (tmtt) cc_final: 0.7435 (tmtt) REVERT: A 864 VAL cc_start: 0.8141 (m) cc_final: 0.7887 (p) REVERT: A 1012 ARG cc_start: 0.7387 (ttp80) cc_final: 0.6955 (ttp80) REVERT: A 1032 PHE cc_start: 0.7843 (t80) cc_final: 0.7617 (t80) REVERT: A 1064 TRP cc_start: 0.7700 (p-90) cc_final: 0.7479 (p-90) REVERT: A 1079 MET cc_start: 0.6093 (mtm) cc_final: 0.5779 (mtm) REVERT: A 1108 GLU cc_start: 0.7539 (pp20) cc_final: 0.7121 (pp20) REVERT: A 1123 GLU cc_start: 0.6944 (pp20) cc_final: 0.6545 (pp20) REVERT: A 1142 GLU cc_start: 0.7550 (tt0) cc_final: 0.7346 (tt0) REVERT: A 1182 ASN cc_start: 0.8030 (m-40) cc_final: 0.7824 (m-40) REVERT: A 1216 GLU cc_start: 0.7194 (pt0) cc_final: 0.6970 (pt0) REVERT: A 1227 GLU cc_start: 0.7145 (pp20) cc_final: 0.6941 (pp20) REVERT: A 1447 ILE cc_start: 0.7940 (pt) cc_final: 0.7723 (mt) REVERT: A 1514 GLU cc_start: 0.7471 (tp30) cc_final: 0.7230 (tp30) REVERT: A 1755 ASP cc_start: 0.7744 (p0) cc_final: 0.7268 (p0) REVERT: A 1845 MET cc_start: 0.5595 (ptm) cc_final: 0.5159 (ptm) outliers start: 9 outliers final: 6 residues processed: 358 average time/residue: 0.3509 time to fit residues: 171.2386 Evaluate side-chains 345 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 339 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1268 ASP Chi-restraints excluded: chain A residue 1441 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 0.2980 chunk 48 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN A1215 GLN A1569 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14860 Z= 0.199 Angle : 0.527 6.567 20234 Z= 0.273 Chirality : 0.040 0.178 2268 Planarity : 0.004 0.053 2438 Dihedral : 12.885 140.070 2464 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.93 % Allowed : 10.95 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.20), residues: 1697 helix: 1.02 (0.19), residues: 806 sheet: -0.21 (0.43), residues: 148 loop : -1.83 (0.20), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 897 HIS 0.010 0.001 HIS A 916 PHE 0.033 0.002 PHE A 82 TYR 0.017 0.002 TYR A 668 ARG 0.007 0.000 ARG A1542 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 347 time to evaluate : 1.548 Fit side-chains revert: symmetry clash REVERT: A 145 LYS cc_start: 0.7212 (mmtt) cc_final: 0.6970 (ttmm) REVERT: A 200 GLU cc_start: 0.7433 (tp30) cc_final: 0.6927 (tp30) REVERT: A 209 ASP cc_start: 0.7020 (m-30) cc_final: 0.6104 (m-30) REVERT: A 213 GLU cc_start: 0.6893 (mp0) cc_final: 0.6589 (mp0) REVERT: A 271 LYS cc_start: 0.7978 (ptpp) cc_final: 0.7413 (ptpp) REVERT: A 298 GLU cc_start: 0.6796 (mm-30) cc_final: 0.6477 (mm-30) REVERT: A 302 CYS cc_start: 0.7852 (t) cc_final: 0.7432 (t) REVERT: A 306 ASP cc_start: 0.7348 (m-30) cc_final: 0.7005 (m-30) REVERT: A 488 GLU cc_start: 0.7268 (tp30) cc_final: 0.6981 (tp30) REVERT: A 489 LYS cc_start: 0.7819 (ttmt) cc_final: 0.7477 (tttt) REVERT: A 707 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.7002 (mp) REVERT: A 719 SER cc_start: 0.8459 (t) cc_final: 0.8220 (t) REVERT: A 830 GLU cc_start: 0.6677 (tt0) cc_final: 0.6435 (tt0) REVERT: A 856 LYS cc_start: 0.7730 (tmtt) cc_final: 0.7454 (tmtt) REVERT: A 864 VAL cc_start: 0.8168 (m) cc_final: 0.7912 (p) REVERT: A 912 LYS cc_start: 0.8575 (ttmm) cc_final: 0.8318 (ttmm) REVERT: A 1012 ARG cc_start: 0.7361 (ttp80) cc_final: 0.7048 (ttp80) REVERT: A 1032 PHE cc_start: 0.7857 (t80) cc_final: 0.7644 (t80) REVERT: A 1064 TRP cc_start: 0.7712 (p-90) cc_final: 0.7445 (p-90) REVERT: A 1079 MET cc_start: 0.6103 (mtm) cc_final: 0.5814 (mtm) REVERT: A 1108 GLU cc_start: 0.7552 (pp20) cc_final: 0.7136 (pp20) REVERT: A 1135 ARG cc_start: 0.7578 (ttp80) cc_final: 0.7377 (ttm-80) REVERT: A 1182 ASN cc_start: 0.8041 (m-40) cc_final: 0.7840 (m-40) REVERT: A 1216 GLU cc_start: 0.7133 (pt0) cc_final: 0.6902 (pt0) REVERT: A 1227 GLU cc_start: 0.7134 (pp20) cc_final: 0.6934 (pp20) REVERT: A 1447 ILE cc_start: 0.7870 (pt) cc_final: 0.7656 (mt) REVERT: A 1514 GLU cc_start: 0.7370 (tp30) cc_final: 0.7033 (tp30) REVERT: A 1755 ASP cc_start: 0.7820 (p0) cc_final: 0.7340 (p0) REVERT: A 1845 MET cc_start: 0.5637 (ptm) cc_final: 0.5289 (ptm) outliers start: 12 outliers final: 9 residues processed: 352 average time/residue: 0.3633 time to fit residues: 173.4721 Evaluate side-chains 352 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 342 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1268 ASP Chi-restraints excluded: chain A residue 1441 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 167 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 HIS ** A1011 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 14860 Z= 0.423 Angle : 0.644 8.892 20234 Z= 0.338 Chirality : 0.046 0.194 2268 Planarity : 0.005 0.054 2438 Dihedral : 13.000 138.844 2464 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.99 % Allowed : 12.48 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.79 (0.19), residues: 1697 helix: 0.61 (0.18), residues: 815 sheet: 0.08 (0.45), residues: 134 loop : -1.97 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 897 HIS 0.011 0.002 HIS A 916 PHE 0.051 0.002 PHE A1048 TYR 0.023 0.003 TYR A1348 ARG 0.009 0.001 ARG A1422 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 390 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7713 (ptp-170) cc_final: 0.7463 (ptp-170) REVERT: A 200 GLU cc_start: 0.7600 (tp30) cc_final: 0.6872 (tp30) REVERT: A 209 ASP cc_start: 0.7062 (m-30) cc_final: 0.6437 (m-30) REVERT: A 271 LYS cc_start: 0.8079 (ptpp) cc_final: 0.7564 (ptpp) REVERT: A 298 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6727 (mm-30) REVERT: A 302 CYS cc_start: 0.7897 (t) cc_final: 0.7507 (t) REVERT: A 306 ASP cc_start: 0.7380 (m-30) cc_final: 0.7020 (m-30) REVERT: A 488 GLU cc_start: 0.7315 (tp30) cc_final: 0.6981 (tp30) REVERT: A 489 LYS cc_start: 0.7872 (ttmt) cc_final: 0.7664 (tttt) REVERT: A 655 ASP cc_start: 0.7256 (t70) cc_final: 0.7048 (t70) REVERT: A 671 MET cc_start: 0.6834 (mmm) cc_final: 0.6555 (tpp) REVERT: A 686 MET cc_start: 0.6865 (mmm) cc_final: 0.6648 (mmt) REVERT: A 719 SER cc_start: 0.8517 (t) cc_final: 0.7759 (p) REVERT: A 856 LYS cc_start: 0.7854 (tmtt) cc_final: 0.7561 (tmtt) REVERT: A 864 VAL cc_start: 0.8251 (m) cc_final: 0.7930 (p) REVERT: A 912 LYS cc_start: 0.8588 (ttmm) cc_final: 0.8294 (ttpp) REVERT: A 1012 ARG cc_start: 0.7299 (ttp80) cc_final: 0.7034 (ttp80) REVERT: A 1032 PHE cc_start: 0.7997 (t80) cc_final: 0.7794 (t80) REVERT: A 1064 TRP cc_start: 0.7938 (p-90) cc_final: 0.7681 (p-90) REVERT: A 1079 MET cc_start: 0.6311 (mtm) cc_final: 0.5948 (mtm) REVERT: A 1106 LEU cc_start: 0.8364 (mt) cc_final: 0.7955 (mt) REVERT: A 1108 GLU cc_start: 0.7525 (pp20) cc_final: 0.7104 (pp20) REVERT: A 1223 THR cc_start: 0.8079 (m) cc_final: 0.7689 (p) REVERT: A 1278 MET cc_start: 0.8179 (mmm) cc_final: 0.7569 (mmm) REVERT: A 1514 GLU cc_start: 0.7319 (tp30) cc_final: 0.7041 (tp30) REVERT: A 1519 GLU cc_start: 0.7119 (tt0) cc_final: 0.6915 (mt-10) REVERT: A 1755 ASP cc_start: 0.8002 (p0) cc_final: 0.7599 (p0) REVERT: A 1778 VAL cc_start: 0.8279 (t) cc_final: 0.7940 (p) outliers start: 28 outliers final: 17 residues processed: 400 average time/residue: 0.3411 time to fit residues: 186.6220 Evaluate side-chains 396 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 379 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1268 ASP Chi-restraints excluded: chain A residue 1441 LEU Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1787 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 142 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 ASN A 914 ASN ** A1011 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14860 Z= 0.191 Angle : 0.557 9.763 20234 Z= 0.287 Chirality : 0.041 0.178 2268 Planarity : 0.004 0.048 2438 Dihedral : 12.863 140.468 2464 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.66 % Allowed : 15.00 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.44 (0.20), residues: 1697 helix: 1.01 (0.19), residues: 797 sheet: 0.21 (0.45), residues: 134 loop : -1.86 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 520 HIS 0.007 0.001 HIS A 916 PHE 0.039 0.002 PHE A 82 TYR 0.013 0.001 TYR A 754 ARG 0.006 0.000 ARG A1542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 369 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7651 (ptp-170) cc_final: 0.7403 (ptp-170) REVERT: A 113 VAL cc_start: 0.7597 (t) cc_final: 0.7260 (p) REVERT: A 200 GLU cc_start: 0.7442 (tp30) cc_final: 0.6871 (tp30) REVERT: A 209 ASP cc_start: 0.6982 (m-30) cc_final: 0.6400 (m-30) REVERT: A 271 LYS cc_start: 0.8022 (ptpp) cc_final: 0.7449 (ptpp) REVERT: A 298 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6628 (mm-30) REVERT: A 302 CYS cc_start: 0.7834 (t) cc_final: 0.7363 (t) REVERT: A 306 ASP cc_start: 0.7374 (m-30) cc_final: 0.7004 (m-30) REVERT: A 488 GLU cc_start: 0.7308 (tp30) cc_final: 0.7015 (tp30) REVERT: A 489 LYS cc_start: 0.7840 (ttmt) cc_final: 0.7617 (tttt) REVERT: A 543 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.7875 (tt) REVERT: A 686 MET cc_start: 0.6636 (mmm) cc_final: 0.6403 (mmt) REVERT: A 719 SER cc_start: 0.8508 (t) cc_final: 0.8245 (t) REVERT: A 856 LYS cc_start: 0.7762 (tmtt) cc_final: 0.7478 (tmtt) REVERT: A 1012 ARG cc_start: 0.7180 (ttp80) cc_final: 0.6970 (ttp80) REVERT: A 1064 TRP cc_start: 0.7787 (p-90) cc_final: 0.7561 (p-90) REVERT: A 1079 MET cc_start: 0.6226 (mtm) cc_final: 0.5951 (mtm) REVERT: A 1108 GLU cc_start: 0.7535 (pp20) cc_final: 0.7028 (pp20) REVERT: A 1123 GLU cc_start: 0.6899 (pp20) cc_final: 0.6314 (pp20) REVERT: A 1135 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7211 (ttt-90) REVERT: A 1216 GLU cc_start: 0.6980 (pt0) cc_final: 0.6774 (pt0) REVERT: A 1371 VAL cc_start: 0.8053 (p) cc_final: 0.7850 (t) REVERT: A 1479 GLU cc_start: 0.7073 (mp0) cc_final: 0.6767 (mp0) REVERT: A 1755 ASP cc_start: 0.7974 (p0) cc_final: 0.7546 (p0) REVERT: A 1777 ARG cc_start: 0.6823 (mtt180) cc_final: 0.6577 (mmt90) REVERT: A 1845 MET cc_start: 0.6093 (ptm) cc_final: 0.5783 (ptm) outliers start: 23 outliers final: 12 residues processed: 380 average time/residue: 0.3693 time to fit residues: 191.3470 Evaluate side-chains 372 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 358 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain A residue 1135 ARG Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1268 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 167 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** A1011 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14860 Z= 0.204 Angle : 0.551 9.245 20234 Z= 0.285 Chirality : 0.041 0.177 2268 Planarity : 0.004 0.050 2438 Dihedral : 12.797 139.780 2464 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.66 % Allowed : 15.53 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.34 (0.20), residues: 1697 helix: 1.11 (0.19), residues: 800 sheet: 0.30 (0.46), residues: 134 loop : -1.84 (0.20), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 897 HIS 0.006 0.001 HIS A1011 PHE 0.023 0.001 PHE A1567 TYR 0.018 0.002 TYR A 754 ARG 0.007 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 360 time to evaluate : 1.726 Fit side-chains revert: symmetry clash REVERT: A 113 VAL cc_start: 0.7602 (t) cc_final: 0.7268 (p) REVERT: A 185 GLN cc_start: 0.7563 (mp10) cc_final: 0.7295 (mp10) REVERT: A 200 GLU cc_start: 0.7476 (tp30) cc_final: 0.6880 (tp30) REVERT: A 209 ASP cc_start: 0.6877 (m-30) cc_final: 0.5760 (m-30) REVERT: A 213 GLU cc_start: 0.6993 (mp0) cc_final: 0.6380 (mp0) REVERT: A 271 LYS cc_start: 0.8024 (ptpp) cc_final: 0.7425 (ptpp) REVERT: A 298 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6659 (mm-30) REVERT: A 302 CYS cc_start: 0.7879 (t) cc_final: 0.7535 (t) REVERT: A 306 ASP cc_start: 0.7379 (m-30) cc_final: 0.7019 (m-30) REVERT: A 488 GLU cc_start: 0.7334 (tp30) cc_final: 0.7036 (tp30) REVERT: A 489 LYS cc_start: 0.7834 (ttmt) cc_final: 0.7544 (tttt) REVERT: A 543 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.7876 (tt) REVERT: A 686 MET cc_start: 0.6646 (mmm) cc_final: 0.6414 (mmt) REVERT: A 719 SER cc_start: 0.8477 (t) cc_final: 0.8227 (t) REVERT: A 856 LYS cc_start: 0.7781 (tmtt) cc_final: 0.7487 (tmtt) REVERT: A 887 MET cc_start: 0.7006 (tmm) cc_final: 0.6421 (tmm) REVERT: A 925 MET cc_start: 0.7253 (mtt) cc_final: 0.7000 (mtm) REVERT: A 1012 ARG cc_start: 0.7191 (ttp80) cc_final: 0.6956 (ttp80) REVERT: A 1064 TRP cc_start: 0.7806 (p-90) cc_final: 0.7546 (p-90) REVERT: A 1108 GLU cc_start: 0.7504 (pp20) cc_final: 0.7045 (pp20) REVERT: A 1123 GLU cc_start: 0.6902 (pp20) cc_final: 0.6323 (pp20) REVERT: A 1135 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7215 (ttt-90) REVERT: A 1264 MET cc_start: 0.6349 (mtm) cc_final: 0.6083 (mtp) REVERT: A 1368 ASN cc_start: 0.7859 (t0) cc_final: 0.7534 (t0) REVERT: A 1479 GLU cc_start: 0.7008 (mp0) cc_final: 0.6614 (mp0) REVERT: A 1514 GLU cc_start: 0.7309 (tp30) cc_final: 0.7021 (tp30) REVERT: A 1755 ASP cc_start: 0.7977 (p0) cc_final: 0.7550 (p0) REVERT: A 1777 ARG cc_start: 0.6822 (mtt180) cc_final: 0.6580 (mmt90) outliers start: 23 outliers final: 17 residues processed: 369 average time/residue: 0.3511 time to fit residues: 175.6983 Evaluate side-chains 377 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 358 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain A residue 1135 ARG Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1268 ASP Chi-restraints excluded: chain A residue 1787 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 93 optimal weight: 0.0770 chunk 166 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** A1011 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14860 Z= 0.197 Angle : 0.542 10.719 20234 Z= 0.280 Chirality : 0.040 0.178 2268 Planarity : 0.004 0.048 2438 Dihedral : 12.742 139.769 2464 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.73 % Allowed : 15.79 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.27 (0.20), residues: 1697 helix: 1.17 (0.19), residues: 800 sheet: 0.34 (0.46), residues: 134 loop : -1.82 (0.20), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 897 HIS 0.007 0.001 HIS A1011 PHE 0.021 0.001 PHE A 265 TYR 0.019 0.002 TYR A 861 ARG 0.007 0.000 ARG A1542 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 358 time to evaluate : 1.578 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7201 (pmm) cc_final: 0.6998 (pmm) REVERT: A 9 ARG cc_start: 0.7679 (ptp-170) cc_final: 0.7453 (ptp-170) REVERT: A 113 VAL cc_start: 0.7612 (t) cc_final: 0.7269 (p) REVERT: A 185 GLN cc_start: 0.7575 (mp10) cc_final: 0.7249 (mp10) REVERT: A 200 GLU cc_start: 0.7466 (tp30) cc_final: 0.6877 (tp30) REVERT: A 209 ASP cc_start: 0.6819 (m-30) cc_final: 0.5650 (m-30) REVERT: A 213 GLU cc_start: 0.6980 (mp0) cc_final: 0.6342 (mp0) REVERT: A 271 LYS cc_start: 0.8023 (ptpp) cc_final: 0.7421 (ptpp) REVERT: A 298 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6656 (mm-30) REVERT: A 302 CYS cc_start: 0.7879 (t) cc_final: 0.7507 (t) REVERT: A 306 ASP cc_start: 0.7389 (m-30) cc_final: 0.7020 (m-30) REVERT: A 488 GLU cc_start: 0.7330 (tp30) cc_final: 0.7039 (tp30) REVERT: A 543 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.7870 (tt) REVERT: A 686 MET cc_start: 0.6646 (mmm) cc_final: 0.6411 (mmt) REVERT: A 719 SER cc_start: 0.8522 (t) cc_final: 0.8252 (t) REVERT: A 848 MET cc_start: 0.7445 (mmm) cc_final: 0.6988 (mmm) REVERT: A 856 LYS cc_start: 0.7769 (tmtt) cc_final: 0.7504 (tmtt) REVERT: A 887 MET cc_start: 0.6997 (tmm) cc_final: 0.6394 (tmm) REVERT: A 925 MET cc_start: 0.7254 (mtt) cc_final: 0.7000 (mtm) REVERT: A 1012 ARG cc_start: 0.7162 (ttp80) cc_final: 0.6916 (ttp80) REVERT: A 1064 TRP cc_start: 0.7791 (p-90) cc_final: 0.7553 (p-90) REVERT: A 1108 GLU cc_start: 0.7514 (pp20) cc_final: 0.7068 (pp20) REVERT: A 1135 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7206 (ttt-90) REVERT: A 1137 LYS cc_start: 0.8391 (mttt) cc_final: 0.7967 (mttt) REVERT: A 1227 GLU cc_start: 0.7275 (pp20) cc_final: 0.6851 (pp20) REVERT: A 1261 PHE cc_start: 0.7992 (t80) cc_final: 0.7620 (t80) REVERT: A 1371 VAL cc_start: 0.7902 (p) cc_final: 0.7662 (t) REVERT: A 1514 GLU cc_start: 0.7274 (tp30) cc_final: 0.6984 (tp30) REVERT: A 1755 ASP cc_start: 0.7976 (p0) cc_final: 0.7553 (p0) REVERT: A 1777 ARG cc_start: 0.6824 (mtt180) cc_final: 0.6567 (mmt90) outliers start: 24 outliers final: 17 residues processed: 365 average time/residue: 0.3506 time to fit residues: 173.5489 Evaluate side-chains 378 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 359 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 756 LYS Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain A residue 1135 ARG Chi-restraints excluded: chain A residue 1268 ASP Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1750 ILE Chi-restraints excluded: chain A residue 1787 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 1.9990 chunk 66 optimal weight: 0.0470 chunk 99 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 82 optimal weight: 0.0970 chunk 15 optimal weight: 9.9990 chunk 131 optimal weight: 0.0270 chunk 151 optimal weight: 5.9990 overall best weight: 0.4334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14860 Z= 0.168 Angle : 0.539 10.527 20234 Z= 0.278 Chirality : 0.040 0.177 2268 Planarity : 0.004 0.052 2438 Dihedral : 12.700 139.924 2464 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.53 % Allowed : 16.12 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.16 (0.20), residues: 1697 helix: 1.27 (0.19), residues: 803 sheet: 0.27 (0.46), residues: 140 loop : -1.78 (0.20), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 897 HIS 0.005 0.001 HIS A1011 PHE 0.028 0.001 PHE A 265 TYR 0.017 0.001 TYR A 861 ARG 0.008 0.000 ARG A1422 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 356 time to evaluate : 1.605 Fit side-chains REVERT: A 113 VAL cc_start: 0.7617 (t) cc_final: 0.7283 (p) REVERT: A 185 GLN cc_start: 0.7610 (mp10) cc_final: 0.7367 (mp10) REVERT: A 200 GLU cc_start: 0.7437 (tp30) cc_final: 0.6905 (tp30) REVERT: A 209 ASP cc_start: 0.6713 (m-30) cc_final: 0.5582 (m-30) REVERT: A 213 GLU cc_start: 0.6963 (mp0) cc_final: 0.6313 (mp0) REVERT: A 271 LYS cc_start: 0.7951 (ptpp) cc_final: 0.7353 (ptpp) REVERT: A 298 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6632 (mm-30) REVERT: A 302 CYS cc_start: 0.7863 (t) cc_final: 0.7504 (t) REVERT: A 306 ASP cc_start: 0.7391 (m-30) cc_final: 0.7027 (m-30) REVERT: A 488 GLU cc_start: 0.7283 (tp30) cc_final: 0.6860 (tp30) REVERT: A 686 MET cc_start: 0.6567 (mmm) cc_final: 0.6344 (mmt) REVERT: A 719 SER cc_start: 0.8512 (t) cc_final: 0.8238 (t) REVERT: A 848 MET cc_start: 0.7386 (mmm) cc_final: 0.6948 (mmm) REVERT: A 856 LYS cc_start: 0.7738 (tmtt) cc_final: 0.7466 (tmtt) REVERT: A 887 MET cc_start: 0.6967 (tmm) cc_final: 0.6393 (tmm) REVERT: A 925 MET cc_start: 0.7208 (mtt) cc_final: 0.6971 (mtm) REVERT: A 1012 ARG cc_start: 0.7136 (ttp80) cc_final: 0.6872 (ttp80) REVERT: A 1064 TRP cc_start: 0.7759 (p-90) cc_final: 0.7526 (p-90) REVERT: A 1087 SER cc_start: 0.8388 (m) cc_final: 0.7928 (p) REVERT: A 1105 LYS cc_start: 0.8407 (mmmt) cc_final: 0.8138 (mmmm) REVERT: A 1108 GLU cc_start: 0.7532 (pp20) cc_final: 0.7060 (pp20) REVERT: A 1135 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7192 (ttt-90) REVERT: A 1137 LYS cc_start: 0.8347 (mttt) cc_final: 0.7966 (mttt) REVERT: A 1227 GLU cc_start: 0.7257 (pp20) cc_final: 0.6853 (pp20) REVERT: A 1514 GLU cc_start: 0.7273 (tp30) cc_final: 0.6985 (tp30) REVERT: A 1755 ASP cc_start: 0.7955 (p0) cc_final: 0.7516 (p0) outliers start: 21 outliers final: 18 residues processed: 362 average time/residue: 0.3546 time to fit residues: 174.2263 Evaluate side-chains 375 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 356 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1128 SER Chi-restraints excluded: chain A residue 1135 ARG Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1268 ASP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1787 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 140 optimal weight: 0.0020 chunk 146 optimal weight: 0.0040 chunk 154 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14860 Z= 0.209 Angle : 0.550 10.102 20234 Z= 0.286 Chirality : 0.041 0.178 2268 Planarity : 0.004 0.051 2438 Dihedral : 12.704 139.320 2464 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.39 % Allowed : 16.79 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.16 (0.20), residues: 1697 helix: 1.26 (0.19), residues: 803 sheet: 0.41 (0.47), residues: 134 loop : -1.78 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 897 HIS 0.008 0.001 HIS A1011 PHE 0.031 0.002 PHE A 265 TYR 0.016 0.002 TYR A 28 ARG 0.006 0.000 ARG A1542 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 359 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 VAL cc_start: 0.7687 (t) cc_final: 0.7348 (p) REVERT: A 145 LYS cc_start: 0.7718 (mmtt) cc_final: 0.7252 (ttmm) REVERT: A 185 GLN cc_start: 0.7583 (mp10) cc_final: 0.7325 (mp10) REVERT: A 200 GLU cc_start: 0.7562 (tp30) cc_final: 0.6809 (tp30) REVERT: A 204 LYS cc_start: 0.7729 (mtmm) cc_final: 0.7407 (mtmm) REVERT: A 209 ASP cc_start: 0.6747 (m-30) cc_final: 0.5578 (m-30) REVERT: A 213 GLU cc_start: 0.6990 (mp0) cc_final: 0.6331 (mp0) REVERT: A 271 LYS cc_start: 0.7960 (ptpp) cc_final: 0.7347 (ptpp) REVERT: A 298 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6693 (mm-30) REVERT: A 302 CYS cc_start: 0.7861 (t) cc_final: 0.7501 (t) REVERT: A 306 ASP cc_start: 0.7401 (m-30) cc_final: 0.7029 (m-30) REVERT: A 488 GLU cc_start: 0.7247 (tp30) cc_final: 0.6841 (tp30) REVERT: A 686 MET cc_start: 0.6649 (mmm) cc_final: 0.6411 (mmt) REVERT: A 719 SER cc_start: 0.8536 (t) cc_final: 0.8258 (t) REVERT: A 848 MET cc_start: 0.7417 (mmm) cc_final: 0.6969 (mmm) REVERT: A 856 LYS cc_start: 0.7769 (tmtt) cc_final: 0.7494 (tmtt) REVERT: A 887 MET cc_start: 0.6967 (tmm) cc_final: 0.6384 (tmm) REVERT: A 925 MET cc_start: 0.7298 (mtt) cc_final: 0.7070 (mtm) REVERT: A 1012 ARG cc_start: 0.7163 (ttp80) cc_final: 0.6898 (ttp80) REVERT: A 1064 TRP cc_start: 0.7798 (p-90) cc_final: 0.7562 (p-90) REVERT: A 1108 GLU cc_start: 0.7532 (pp20) cc_final: 0.7066 (pp20) REVERT: A 1135 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7202 (ttt-90) REVERT: A 1137 LYS cc_start: 0.8322 (mttt) cc_final: 0.7971 (mttt) REVERT: A 1227 GLU cc_start: 0.7272 (pp20) cc_final: 0.6886 (pp20) REVERT: A 1514 GLU cc_start: 0.7273 (tp30) cc_final: 0.6981 (tp30) REVERT: A 1755 ASP cc_start: 0.7976 (p0) cc_final: 0.7574 (p0) REVERT: A 1845 MET cc_start: 0.5963 (ptm) cc_final: 0.5407 (ptm) outliers start: 19 outliers final: 17 residues processed: 363 average time/residue: 0.3587 time to fit residues: 176.0759 Evaluate side-chains 374 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 356 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1135 ARG Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1268 ASP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1787 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 114 optimal weight: 0.2980 chunk 172 optimal weight: 4.9990 chunk 158 optimal weight: 0.0670 chunk 137 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14860 Z= 0.196 Angle : 0.554 9.911 20234 Z= 0.286 Chirality : 0.040 0.179 2268 Planarity : 0.004 0.053 2438 Dihedral : 12.696 139.242 2464 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.33 % Allowed : 17.19 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.15 (0.20), residues: 1697 helix: 1.28 (0.19), residues: 802 sheet: 0.31 (0.46), residues: 140 loop : -1.78 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 897 HIS 0.008 0.001 HIS A1011 PHE 0.037 0.001 PHE A 265 TYR 0.014 0.002 TYR A 474 ARG 0.008 0.000 ARG A1422 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3394 Ramachandran restraints generated. 1697 Oldfield, 0 Emsley, 1697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 354 time to evaluate : 1.675 Fit side-chains revert: symmetry clash REVERT: A 113 VAL cc_start: 0.7698 (t) cc_final: 0.7354 (p) REVERT: A 185 GLN cc_start: 0.7611 (mp10) cc_final: 0.7374 (mp10) REVERT: A 200 GLU cc_start: 0.7526 (tp30) cc_final: 0.6781 (tp30) REVERT: A 202 TYR cc_start: 0.7639 (t80) cc_final: 0.7432 (t80) REVERT: A 204 LYS cc_start: 0.7805 (mtmm) cc_final: 0.7357 (mtmm) REVERT: A 209 ASP cc_start: 0.6708 (m-30) cc_final: 0.5748 (m-30) REVERT: A 213 GLU cc_start: 0.6996 (mp0) cc_final: 0.6364 (mp0) REVERT: A 271 LYS cc_start: 0.7917 (ptpp) cc_final: 0.7327 (ptpp) REVERT: A 298 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6712 (mm-30) REVERT: A 302 CYS cc_start: 0.7860 (t) cc_final: 0.7477 (t) REVERT: A 306 ASP cc_start: 0.7393 (m-30) cc_final: 0.7020 (m-30) REVERT: A 488 GLU cc_start: 0.7272 (tp30) cc_final: 0.6879 (tp30) REVERT: A 489 LYS cc_start: 0.7826 (ttmt) cc_final: 0.7460 (ttmt) REVERT: A 686 MET cc_start: 0.6638 (mmm) cc_final: 0.6397 (mmt) REVERT: A 719 SER cc_start: 0.8546 (t) cc_final: 0.8276 (t) REVERT: A 848 MET cc_start: 0.7416 (mmm) cc_final: 0.6976 (mmm) REVERT: A 856 LYS cc_start: 0.7741 (tmtt) cc_final: 0.7467 (tmtt) REVERT: A 887 MET cc_start: 0.6970 (tmm) cc_final: 0.6383 (tmm) REVERT: A 925 MET cc_start: 0.7294 (mtt) cc_final: 0.7065 (mtm) REVERT: A 1012 ARG cc_start: 0.7185 (ttp80) cc_final: 0.6897 (ttp80) REVERT: A 1032 PHE cc_start: 0.7875 (t80) cc_final: 0.7618 (t80) REVERT: A 1052 MET cc_start: 0.7486 (mtt) cc_final: 0.7205 (mtp) REVERT: A 1064 TRP cc_start: 0.7802 (p-90) cc_final: 0.7536 (p-90) REVERT: A 1105 LYS cc_start: 0.8431 (mmmt) cc_final: 0.8136 (mmmm) REVERT: A 1108 GLU cc_start: 0.7544 (pp20) cc_final: 0.7061 (pp20) REVERT: A 1135 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7196 (ttt-90) REVERT: A 1137 LYS cc_start: 0.8324 (mttt) cc_final: 0.7970 (mttt) REVERT: A 1227 GLU cc_start: 0.7265 (pp20) cc_final: 0.6880 (pp20) REVERT: A 1514 GLU cc_start: 0.7273 (tp30) cc_final: 0.6965 (tp30) REVERT: A 1755 ASP cc_start: 0.7984 (p0) cc_final: 0.7567 (p0) REVERT: A 1845 MET cc_start: 0.5949 (ptm) cc_final: 0.5366 (ptm) outliers start: 18 outliers final: 17 residues processed: 360 average time/residue: 0.3669 time to fit residues: 180.7618 Evaluate side-chains 370 residues out of total 1499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 352 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 910 LEU Chi-restraints excluded: chain A residue 1122 ILE Chi-restraints excluded: chain A residue 1135 ARG Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1268 ASP Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1738 ILE Chi-restraints excluded: chain A residue 1787 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.0170 chunk 42 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 141 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 120 optimal weight: 2.9990 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 ASN A 914 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1035 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.135368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.110386 restraints weight = 58602.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.116150 restraints weight = 20534.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.119765 restraints weight = 9938.854| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 14860 Z= 0.288 Angle : 0.592 10.271 20234 Z= 0.307 Chirality : 0.042 0.182 2268 Planarity : 0.004 0.050 2438 Dihedral : 12.764 137.974 2464 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.46 % Allowed : 17.05 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.31 (0.20), residues: 1697 helix: 1.16 (0.19), residues: 798 sheet: 0.31 (0.46), residues: 134 loop : -1.87 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 897 HIS 0.011 0.001 HIS A1011 PHE 0.040 0.002 PHE A 265 TYR 0.018 0.002 TYR A 28 ARG 0.008 0.000 ARG A1422 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4012.97 seconds wall clock time: 72 minutes 49.96 seconds (4369.96 seconds total)