Starting phenix.real_space_refine on Fri May 10 19:31:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6y_18969/05_2024/8r6y_18969_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6y_18969/05_2024/8r6y_18969.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6y_18969/05_2024/8r6y_18969_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6y_18969/05_2024/8r6y_18969_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6y_18969/05_2024/8r6y_18969_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6y_18969/05_2024/8r6y_18969.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6y_18969/05_2024/8r6y_18969.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6y_18969/05_2024/8r6y_18969_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r6y_18969/05_2024/8r6y_18969_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 41 5.49 5 Mg 1 5.21 5 S 95 5.16 5 C 10394 2.51 5 N 2912 2.21 5 O 3222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 274": "OE1" <-> "OE2" Residue "A PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1982": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 16665 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 15811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1991, 15811 Classifications: {'peptide': 1991} Link IDs: {'PCIS': 2, 'PTRANS': 70, 'TRANS': 1918} Chain breaks: 7 Chain: "P" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 341 Classifications: {'RNA': 16} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 12} Chain: "T" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 324 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 12} 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: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 95 Unusual residues: {'M7G': 1} Classifications: {'RNA': 3, 'undetermined': 1} Modifications used: {'rna2p_pur': 3} Link IDs: {'rna2p': 2, None: 1} Not linked: pdbres="M7G C 1 " pdbres=" A C 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: 9.38, per 1000 atoms: 0.56 Number of scatterers: 16665 At special positions: 0 Unit cell: (106.53, 132.66, 121.27, 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 95 16.00 P 41 15.00 Mg 1 11.99 O 3222 8.00 N 2912 7.00 C 10394 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.74 Conformation dependent library (CDL) restraints added in 3.0 seconds 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3722 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 14 sheets defined 45.1% alpha, 7.3% beta 9 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 8.83 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 78 through 83 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 135 through 157 removed outlier: 3.837A pdb=" N TYR A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 185 through 205 Processing helix chain 'A' and resid 219 through 233 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 284 Processing helix chain 'A' and resid 293 through 317 Processing helix chain 'A' and resid 352 through 358 removed outlier: 3.859A pdb=" N MET A 356 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP A 357 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 373 removed outlier: 3.594A pdb=" N ASP A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A 372 " --> pdb=" O CYS A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 392 Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.751A 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 458 through 464 removed outlier: 3.534A pdb=" N LEU A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 492 removed outlier: 3.557A pdb=" N ALA A 492 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 513 through 532 Processing helix chain 'A' and resid 604 through 610 removed outlier: 3.565A pdb=" N THR A 607 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASN A 608 " --> pdb=" O LYS A 605 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 609 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 639 through 654 Processing helix chain 'A' and resid 657 through 674 removed outlier: 3.929A pdb=" N GLU A 661 " --> pdb=" O SER A 657 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A 662 " --> pdb=" O LYS A 658 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A 663 " --> pdb=" O THR A 659 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 666 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TYR A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N GLY A 673 " --> pdb=" O THR A 669 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N PHE A 674 " --> pdb=" O GLN A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 690 removed outlier: 4.009A pdb=" N LEU A 687 " --> pdb=" O GLN A 684 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY A 688 " --> pdb=" O LYS A 685 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 689 " --> pdb=" O MET A 686 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 690 " --> pdb=" O LEU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 715 Processing helix chain 'A' and resid 743 through 754 removed outlier: 4.138A pdb=" N TYR A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLY A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR A 754 " --> pdb=" O TRP A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 779 removed outlier: 4.509A pdb=" N MET A 777 " --> pdb=" O LYS A 773 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU A 778 " --> pdb=" O ILE A 774 " (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 820 Processing helix chain 'A' and resid 825 through 838 Processing helix chain 'A' and resid 842 through 845 No H-bonds generated for 'chain 'A' and resid 842 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 884 removed outlier: 3.502A pdb=" N THR A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 881 " --> pdb=" O LYS A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 903 removed outlier: 3.710A pdb=" N VAL A 893 " --> pdb=" O TYR A 889 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLY A 894 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLN A 895 " --> pdb=" O ASP A 891 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 896 " --> pdb=" O ALA A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 946 removed outlier: 4.251A pdb=" N GLY A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU A 946 " --> pdb=" O CYS A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 972 removed outlier: 3.877A pdb=" N GLY A 966 " --> pdb=" O GLU A 963 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 972 " --> pdb=" O SER A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1004 Processing helix chain 'A' and resid 1011 through 1021 removed outlier: 4.526A pdb=" N PHE A1021 " --> pdb=" O ALA A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1038 removed outlier: 3.926A pdb=" N SER A1038 " --> pdb=" O ALA A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1057 Processing helix chain 'A' and resid 1084 through 1107 Processing helix chain 'A' and resid 1140 through 1159 removed outlier: 4.159A pdb=" N VAL A1156 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LYS A1157 " --> pdb=" O LEU A1153 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE A1158 " --> pdb=" O HIS A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1199 No H-bonds generated for 'chain 'A' and resid 1196 through 1199' Processing helix chain 'A' and resid 1211 through 1227 Processing helix chain 'A' and resid 1232 through 1249 Processing helix chain 'A' and resid 1258 through 1267 removed outlier: 4.817A pdb=" N SER A1267 " --> pdb=" O GLY A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1299 Processing helix chain 'A' and resid 1302 through 1314 Processing helix chain 'A' and resid 1343 through 1355 removed outlier: 4.653A pdb=" N LYS A1347 " --> pdb=" O GLY A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1367 Processing helix chain 'A' and resid 1369 through 1373 removed outlier: 3.566A pdb=" N LEU A1372 " --> pdb=" O PRO A1369 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR A1373 " --> pdb=" O GLY A1370 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1369 through 1373' Processing helix chain 'A' and resid 1379 through 1390 Processing helix chain 'A' and resid 1395 through 1398 No H-bonds generated for 'chain 'A' and resid 1395 through 1398' Processing helix chain 'A' and resid 1404 through 1413 removed outlier: 3.680A pdb=" N VAL A1413 " --> pdb=" O VAL A1409 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1446 Processing helix chain 'A' and resid 1449 through 1451 No H-bonds generated for 'chain 'A' and resid 1449 through 1451' Processing helix chain 'A' and resid 1458 through 1464 Processing helix chain 'A' and resid 1468 through 1480 removed outlier: 4.681A pdb=" N GLU A1480 " --> pdb=" O THR A1476 " (cutoff:3.500A) 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 1558 removed outlier: 3.827A pdb=" N LEU A1556 " --> pdb=" O PRO A1552 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG A1557 " --> pdb=" O SER A1553 " (cutoff:3.500A) Processing helix chain 'A' and resid 1564 through 1573 Processing helix chain 'A' and resid 1596 through 1603 Processing helix chain 'A' and resid 1617 through 1623 removed outlier: 4.190A pdb=" N GLU A1621 " --> pdb=" O LEU A1617 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG A1622 " --> pdb=" O ASP A1618 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1637 Processing helix chain 'A' and resid 1643 through 1656 Processing helix chain 'A' and resid 1670 through 1682 Processing helix chain 'A' and resid 1688 through 1695 Processing helix chain 'A' and resid 1759 through 1772 Processing helix chain 'A' and resid 1821 through 1823 No H-bonds generated for 'chain 'A' and resid 1821 through 1823' Processing helix chain 'A' and resid 1859 through 1867 Processing helix chain 'A' and resid 1873 through 1875 No H-bonds generated for 'chain 'A' and resid 1873 through 1875' Processing helix chain 'A' and resid 1891 through 1902 Processing helix chain 'A' and resid 1915 through 1930 removed outlier: 3.695A pdb=" N GLN A1930 " --> pdb=" O SER A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1953 through 1956 No H-bonds generated for 'chain 'A' and resid 1953 through 1956' Processing helix chain 'A' and resid 1998 through 2004 removed outlier: 3.568A pdb=" N VAL A2003 " --> pdb=" O GLY A1999 " (cutoff:3.500A) Processing helix chain 'A' and resid 2016 through 2026 removed outlier: 3.923A pdb=" N ALA A2024 " --> pdb=" O ILE A2020 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A2025 " --> pdb=" O THR A2021 " (cutoff:3.500A) Processing helix chain 'A' and resid 2028 through 2037 removed outlier: 3.953A pdb=" N ARG A2032 " --> pdb=" O LYS A2028 " (cutoff:3.500A) Processing helix chain 'A' and resid 2042 through 2054 removed outlier: 4.648A pdb=" N GLN A2047 " --> pdb=" O ALA A2043 " (cutoff:3.500A) Proline residue: A2050 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 22 through 24 removed outlier: 6.438A pdb=" N ILE A 122 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLY A 168 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL A 124 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE A 170 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLU A 126 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL A 172 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER A 128 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 125 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 113 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 36 through 40 removed outlier: 3.582A pdb=" N THR A 39 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 409 through 412 removed outlier: 4.647A pdb=" N ARG A 409 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 543 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N GLU A 540 " --> pdb=" O PRO A 557 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 588 through 590 Processing sheet with id= E, first strand: chain 'A' and resid 719 through 721 removed outlier: 3.586A pdb=" N GLU A 728 " --> pdb=" O ILE A 721 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 908 through 913 removed outlier: 3.650A pdb=" N LYS A 913 " --> pdb=" O ARG A 920 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG A 920 " --> pdb=" O LYS A 913 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 978 through 984 removed outlier: 3.726A pdb=" N SER A1128 " --> pdb=" O ASN A 984 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1025 through 1027 Processing sheet with id= I, first strand: chain 'A' and resid 1178 through 1180 Processing sheet with id= J, first strand: chain 'A' and resid 1337 through 1339 Processing sheet with id= K, first strand: chain 'A' and resid 1500 through 1502 removed outlier: 3.654A pdb=" N LEU A1502 " --> pdb=" O ARG A1579 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A1579 " --> pdb=" O LEU A1502 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1699 through 1705 removed outlier: 6.836A pdb=" N VAL A1724 " --> pdb=" O SER A1704 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A1721 " --> pdb=" O GLY A1740 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A1727 " --> pdb=" O VAL A1734 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASP A1739 " --> pdb=" O LEU A1747 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU A1747 " --> pdb=" O ASP A1739 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1789 through 1791 Processing sheet with id= N, first strand: chain 'A' and resid 1827 through 1829 611 hydrogen bonds defined for protein. 1752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 7.98 Time building geometry restraints manager: 7.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2654 1.30 - 1.43: 4627 1.43 - 1.56: 9568 1.56 - 1.68: 77 1.68 - 1.81: 156 Bond restraints: 17082 Sorted by residual: bond pdb=" C3' 2KH A2101 " pdb=" C4' 2KH A2101 " ideal model delta sigma weight residual 1.643 1.305 0.338 2.00e-02 2.50e+03 2.86e+02 bond pdb=" C4' 2KH A2101 " pdb=" O4' 2KH A2101 " ideal model delta sigma weight residual 1.310 1.609 -0.299 2.00e-02 2.50e+03 2.24e+02 bond pdb=" C1' 2KH A2101 " pdb=" O4' 2KH A2101 " ideal model delta sigma weight residual 1.561 1.304 0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" C3' M7G C 1 " pdb=" C4' M7G C 1 " ideal model delta sigma weight residual 1.305 1.522 -0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C2' 2KH A2101 " pdb=" C3' 2KH A2101 " ideal model delta sigma weight residual 1.312 1.527 -0.215 2.00e-02 2.50e+03 1.15e+02 ... (remaining 17077 not shown) Histogram of bond angle deviations from ideal: 80.59 - 91.29: 3 91.29 - 102.00: 97 102.00 - 112.70: 9483 112.70 - 123.41: 12919 123.41 - 134.11: 740 Bond angle restraints: 23242 Sorted by residual: angle pdb=" O3A M7G C 1 " pdb=" PA M7G C 1 " pdb=" O5' M7G C 1 " ideal model delta sigma weight residual 109.47 80.59 28.88 3.00e+00 1.11e-01 9.27e+01 angle pdb=" O2A M7G C 1 " pdb=" PA M7G C 1 " pdb=" O3A M7G C 1 " ideal model delta sigma weight residual 109.47 85.81 23.66 3.00e+00 1.11e-01 6.22e+01 angle pdb=" C1' M7G C 1 " pdb=" N9 M7G C 1 " pdb=" C4 M7G C 1 " ideal model delta sigma weight residual 103.02 125.92 -22.90 3.00e+00 1.11e-01 5.83e+01 angle pdb=" O4' A C 2 " pdb=" C1' A C 2 " pdb=" C2' A C 2 " ideal model delta sigma weight residual 105.80 99.22 6.58 1.00e+00 1.00e+00 4.33e+01 angle pdb=" O1A M7G C 1 " pdb=" PA M7G C 1 " pdb=" O3A M7G C 1 " ideal model delta sigma weight residual 109.47 90.80 18.67 3.00e+00 1.11e-01 3.87e+01 ... (remaining 23237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 9972 35.35 - 70.71: 321 70.71 - 106.06: 27 106.06 - 141.42: 0 141.42 - 176.77: 5 Dihedral angle restraints: 10325 sinusoidal: 4565 harmonic: 5760 Sorted by residual: dihedral pdb=" C5' A C 3 " pdb=" C4' A C 3 " pdb=" C3' A C 3 " pdb=" O3' A C 3 " ideal model delta sinusoidal sigma weight residual 147.00 82.02 64.98 1 8.00e+00 1.56e-02 8.66e+01 dihedral pdb=" O4' U T 18 " pdb=" C1' U T 18 " pdb=" N1 U T 18 " pdb=" C2 U T 18 " ideal model delta sinusoidal sigma weight residual 200.00 33.10 166.90 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" C4' A C 3 " pdb=" C3' A C 3 " pdb=" C2' A C 3 " pdb=" C1' A C 3 " ideal model delta sinusoidal sigma weight residual -35.00 25.99 -60.99 1 8.00e+00 1.56e-02 7.72e+01 ... (remaining 10322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.196: 2593 0.196 - 0.393: 7 0.393 - 0.589: 1 0.589 - 0.785: 0 0.785 - 0.981: 1 Chirality restraints: 2602 Sorted by residual: chirality pdb=" C1' A C 3 " pdb=" O4' A C 3 " pdb=" C2' A C 3 " pdb=" N9 A C 3 " both_signs ideal model delta sigma weight residual False 2.44 1.46 0.98 2.00e-01 2.50e+01 2.41e+01 chirality pdb=" C3' M7G C 1 " pdb=" C2' M7G C 1 " pdb=" C4' M7G C 1 " pdb=" O3' M7G C 1 " both_signs ideal model delta sigma weight residual False -2.39 -2.79 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" P A C 3 " pdb=" OP1 A C 3 " pdb=" OP2 A C 3 " pdb=" O5' A C 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.80 -0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 2599 not shown) Planarity restraints: 2819 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A1160 " 0.044 5.00e-02 4.00e+02 6.61e-02 7.00e+00 pdb=" N PRO A1161 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A1161 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1161 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U T 22 " -0.027 2.00e-02 2.50e+03 1.48e-02 4.90e+00 pdb=" N1 U T 22 " 0.033 2.00e-02 2.50e+03 pdb=" C2 U T 22 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U T 22 " 0.004 2.00e-02 2.50e+03 pdb=" N3 U T 22 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U T 22 " -0.002 2.00e-02 2.50e+03 pdb=" O4 U T 22 " -0.009 2.00e-02 2.50e+03 pdb=" C5 U T 22 " 0.006 2.00e-02 2.50e+03 pdb=" C6 U T 22 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C T 10 " 0.026 2.00e-02 2.50e+03 1.45e-02 4.73e+00 pdb=" N1 C T 10 " -0.033 2.00e-02 2.50e+03 pdb=" C2 C T 10 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C T 10 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C T 10 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C T 10 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C T 10 " 0.009 2.00e-02 2.50e+03 pdb=" C5 C T 10 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C T 10 " -0.004 2.00e-02 2.50e+03 ... (remaining 2816 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 178 2.60 - 3.18: 13834 3.18 - 3.75: 26580 3.75 - 4.33: 34438 4.33 - 4.90: 57031 Nonbonded interactions: 132061 Sorted by model distance: nonbonded pdb=" O3B 2KH A2101 " pdb="MG MG A2102 " model vdw 2.029 2.170 nonbonded pdb=" O1A 2KH A2101 " pdb="MG MG A2102 " model vdw 2.186 2.170 nonbonded pdb=" O2 C P 14 " pdb=" N2 G T 12 " model vdw 2.232 2.496 nonbonded pdb=" OG1 THR A 558 " pdb=" O HIS A 563 " model vdw 2.246 2.440 nonbonded pdb=" O MET A1729 " pdb=" OG1 THR A1732 " model vdw 2.262 2.440 ... (remaining 132056 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.710 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 50.600 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 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 : 0.007 0.338 17082 Z= 0.344 Angle : 0.736 28.881 23242 Z= 0.354 Chirality : 0.047 0.981 2602 Planarity : 0.004 0.066 2819 Dihedral : 16.451 176.771 6603 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.38 % Allowed : 9.81 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.60 (0.18), residues: 1975 helix: 0.85 (0.17), residues: 916 sheet: -0.46 (0.38), residues: 191 loop : -1.79 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1894 HIS 0.003 0.001 HIS A 447 PHE 0.009 0.001 PHE A1148 TYR 0.010 0.001 TYR A1101 ARG 0.002 0.000 ARG A 667 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 174 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.8308 (ptm) cc_final: 0.8020 (tpp) REVERT: A 274 GLU cc_start: 0.8717 (tp30) cc_final: 0.8477 (tp30) REVERT: A 356 MET cc_start: 0.9045 (mpp) cc_final: 0.8825 (mpp) REVERT: A 406 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.8023 (mt) REVERT: A 436 MET cc_start: 0.8505 (mpp) cc_final: 0.8183 (mpp) REVERT: A 777 MET cc_start: 0.7819 (tpp) cc_final: 0.7394 (tpp) REVERT: A 1270 ASP cc_start: 0.8275 (t70) cc_final: 0.7971 (t0) REVERT: A 1515 ASP cc_start: 0.8843 (m-30) cc_final: 0.8431 (m-30) REVERT: A 1524 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8880 (pp) REVERT: A 1672 MET cc_start: 0.8828 (tmm) cc_final: 0.8594 (tmm) REVERT: A 1694 ARG cc_start: 0.8601 (tmm160) cc_final: 0.8025 (tmm160) REVERT: A 1752 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8634 (tt) REVERT: A 1832 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7762 (mm) REVERT: A 1845 MET cc_start: 0.8487 (tpt) cc_final: 0.8276 (tpt) REVERT: A 1868 ASN cc_start: 0.8506 (m-40) cc_final: 0.8221 (p0) REVERT: A 1896 HIS cc_start: 0.9385 (t70) cc_final: 0.9155 (t-170) REVERT: A 1913 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7308 (ttp80) REVERT: A 1924 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7418 (tm-30) REVERT: A 2022 MET cc_start: 0.8922 (tmm) cc_final: 0.8720 (tmm) REVERT: A 2026 MET cc_start: 0.8980 (tpt) cc_final: 0.8521 (tpp) outliers start: 59 outliers final: 19 residues processed: 226 average time/residue: 0.3059 time to fit residues: 105.1463 Evaluate side-chains 168 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 913 LYS Chi-restraints excluded: chain A residue 991 GLN Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1278 MET Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1519 GLU Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1743 THR Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1832 ILE Chi-restraints excluded: chain A residue 1908 GLN Chi-restraints excluded: chain A residue 1913 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 0.9980 chunk 152 optimal weight: 0.3980 chunk 84 optimal weight: 0.0170 chunk 52 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 60 optimal weight: 0.0170 chunk 95 optimal weight: 10.0000 chunk 117 optimal weight: 0.7980 chunk 182 optimal weight: 20.0000 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 HIS A 757 ASN A 928 ASN ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 ASN A1775 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17082 Z= 0.120 Angle : 0.507 8.593 23242 Z= 0.256 Chirality : 0.037 0.252 2602 Planarity : 0.003 0.058 2819 Dihedral : 14.554 168.502 2772 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.24 % Allowed : 14.00 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.18), residues: 1975 helix: 1.38 (0.18), residues: 916 sheet: -0.24 (0.38), residues: 183 loop : -1.77 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1894 HIS 0.011 0.001 HIS A1483 PHE 0.011 0.001 PHE A1465 TYR 0.012 0.001 TYR A 923 ARG 0.005 0.000 ARG A1493 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 159 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 GLU cc_start: 0.8711 (tp30) cc_final: 0.8448 (tp30) REVERT: A 777 MET cc_start: 0.8004 (tpp) cc_final: 0.7595 (tpp) REVERT: A 1080 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8356 (mm-40) REVERT: A 1270 ASP cc_start: 0.8303 (t70) cc_final: 0.7974 (t0) REVERT: A 1515 ASP cc_start: 0.8845 (m-30) cc_final: 0.8487 (m-30) REVERT: A 1672 MET cc_start: 0.8811 (tmm) cc_final: 0.8577 (tmm) REVERT: A 1694 ARG cc_start: 0.8583 (tmm160) cc_final: 0.8012 (tmm160) REVERT: A 1807 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6593 (ptp-170) REVERT: A 1845 MET cc_start: 0.8498 (tpt) cc_final: 0.8290 (tpt) REVERT: A 1868 ASN cc_start: 0.8524 (m-40) cc_final: 0.8186 (p0) REVERT: A 1896 HIS cc_start: 0.9414 (t70) cc_final: 0.9212 (t-170) REVERT: A 1924 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7310 (tm-30) REVERT: A 2022 MET cc_start: 0.8929 (tmm) cc_final: 0.8664 (tmm) REVERT: A 2026 MET cc_start: 0.8939 (tpt) cc_final: 0.8391 (tpp) outliers start: 39 outliers final: 19 residues processed: 190 average time/residue: 0.3188 time to fit residues: 92.1804 Evaluate side-chains 163 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 142 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1080 GLN Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1197 ARG Chi-restraints excluded: chain A residue 1278 MET Chi-restraints excluded: chain A residue 1297 CYS Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1519 GLU Chi-restraints excluded: chain A residue 1807 ARG Chi-restraints excluded: chain A residue 1846 ASN Chi-restraints excluded: chain A residue 1908 GLN Chi-restraints excluded: chain A residue 2054 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 182 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 chunk 162 optimal weight: 0.0070 chunk 181 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 overall best weight: 2.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 757 ASN ** A1160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17082 Z= 0.188 Angle : 0.501 8.045 23242 Z= 0.256 Chirality : 0.037 0.199 2602 Planarity : 0.003 0.060 2819 Dihedral : 14.329 169.377 2741 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.44 % Allowed : 14.11 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.08 (0.19), residues: 1975 helix: 1.67 (0.18), residues: 912 sheet: -0.31 (0.37), residues: 192 loop : -1.70 (0.18), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1894 HIS 0.004 0.001 HIS A1483 PHE 0.009 0.001 PHE A 911 TYR 0.009 0.001 TYR A 923 ARG 0.005 0.000 ARG A 823 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 137 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 GLU cc_start: 0.8724 (tp30) cc_final: 0.8455 (tp30) REVERT: A 777 MET cc_start: 0.8043 (tpp) cc_final: 0.7569 (tpp) REVERT: A 1197 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8822 (ttp-170) REVERT: A 1270 ASP cc_start: 0.8351 (t70) cc_final: 0.8075 (t0) REVERT: A 1381 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: A 1491 ARG cc_start: 0.8407 (ttp-170) cc_final: 0.8181 (mtm-85) REVERT: A 1524 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8881 (pp) REVERT: A 1672 MET cc_start: 0.8845 (tmm) cc_final: 0.8599 (tmm) REVERT: A 1694 ARG cc_start: 0.8585 (tmm160) cc_final: 0.7986 (tmm160) REVERT: A 1845 MET cc_start: 0.8496 (tpt) cc_final: 0.8294 (tpt) REVERT: A 1868 ASN cc_start: 0.8537 (m-40) cc_final: 0.8163 (p0) REVERT: A 1896 HIS cc_start: 0.9400 (t70) cc_final: 0.9182 (t-170) REVERT: A 1924 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7335 (tm-30) REVERT: A 2022 MET cc_start: 0.8955 (tmm) cc_final: 0.8680 (tmm) REVERT: A 2026 MET cc_start: 0.8908 (tpt) cc_final: 0.8302 (tpp) outliers start: 60 outliers final: 35 residues processed: 185 average time/residue: 0.2912 time to fit residues: 84.0208 Evaluate side-chains 172 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 134 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 757 ASN Chi-restraints excluded: chain A residue 841 ASN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1197 ARG Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1278 MET Chi-restraints excluded: chain A residue 1297 CYS Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1519 GLU Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1846 ASN Chi-restraints excluded: chain A residue 2004 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 180 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 194 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 ASN A 563 HIS A 644 GLN A 928 ASN ** A1834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 17082 Z= 0.402 Angle : 0.624 8.051 23242 Z= 0.320 Chirality : 0.041 0.204 2602 Planarity : 0.004 0.064 2819 Dihedral : 14.345 173.123 2737 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.19 % Allowed : 14.69 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.19), residues: 1975 helix: 1.41 (0.17), residues: 916 sheet: -0.36 (0.38), residues: 185 loop : -1.76 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 520 HIS 0.006 0.001 HIS A1091 PHE 0.016 0.002 PHE A1187 TYR 0.013 0.002 TYR A1218 ARG 0.005 0.000 ARG A1023 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 132 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 GLU cc_start: 0.8753 (tp30) cc_final: 0.8482 (tp30) REVERT: A 406 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7977 (mt) REVERT: A 777 MET cc_start: 0.8115 (tpp) cc_final: 0.7660 (tpp) REVERT: A 800 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8337 (mp0) REVERT: A 1270 ASP cc_start: 0.8349 (t70) cc_final: 0.8115 (t0) REVERT: A 1396 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8707 (t) REVERT: A 1524 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8851 (pp) REVERT: A 1694 ARG cc_start: 0.8614 (tmm160) cc_final: 0.8060 (tmm160) REVERT: A 1845 MET cc_start: 0.8489 (tpt) cc_final: 0.8261 (tpt) REVERT: A 1896 HIS cc_start: 0.9404 (t70) cc_final: 0.9203 (t-170) REVERT: A 1924 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7372 (tm-30) REVERT: A 2022 MET cc_start: 0.8962 (tmm) cc_final: 0.8680 (tmm) REVERT: A 2026 MET cc_start: 0.8879 (tpt) cc_final: 0.8170 (tpp) outliers start: 73 outliers final: 42 residues processed: 195 average time/residue: 0.2905 time to fit residues: 87.9061 Evaluate side-chains 174 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 128 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 841 ASN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1297 CYS Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1807 ARG Chi-restraints excluded: chain A residue 1846 ASN Chi-restraints excluded: chain A residue 1856 ASP Chi-restraints excluded: chain A residue 1950 THR Chi-restraints excluded: chain A residue 2004 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 161 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 144 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1868 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17082 Z= 0.207 Angle : 0.520 7.470 23242 Z= 0.263 Chirality : 0.038 0.196 2602 Planarity : 0.003 0.059 2819 Dihedral : 14.256 172.961 2729 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.16 % Allowed : 16.70 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.06 (0.19), residues: 1975 helix: 1.62 (0.18), residues: 926 sheet: -0.26 (0.39), residues: 188 loop : -1.73 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 520 HIS 0.004 0.001 HIS A1091 PHE 0.009 0.001 PHE A1634 TYR 0.010 0.001 TYR A 923 ARG 0.004 0.000 ARG A1783 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 136 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.8730 (tpp) cc_final: 0.8452 (tpt) REVERT: A 274 GLU cc_start: 0.8725 (tp30) cc_final: 0.8433 (tp30) REVERT: A 356 MET cc_start: 0.9045 (mpp) cc_final: 0.8828 (pmm) REVERT: A 800 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8282 (mp0) REVERT: A 1264 MET cc_start: 0.8536 (ttm) cc_final: 0.8298 (ttt) REVERT: A 1270 ASP cc_start: 0.8325 (t70) cc_final: 0.8087 (t0) REVERT: A 1381 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: A 1396 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8753 (t) REVERT: A 1694 ARG cc_start: 0.8607 (tmm160) cc_final: 0.8064 (tmm160) REVERT: A 1845 MET cc_start: 0.8497 (tpt) cc_final: 0.8248 (tpt) REVERT: A 1868 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8241 (p0) REVERT: A 1896 HIS cc_start: 0.9378 (t70) cc_final: 0.9142 (t-170) REVERT: A 1924 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7198 (tm-30) REVERT: A 2011 HIS cc_start: 0.8523 (m90) cc_final: 0.8254 (m90) REVERT: A 2026 MET cc_start: 0.8874 (tpt) cc_final: 0.8255 (tpp) outliers start: 55 outliers final: 38 residues processed: 180 average time/residue: 0.2854 time to fit residues: 80.5703 Evaluate side-chains 173 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 131 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 841 ASN Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1278 MET Chi-restraints excluded: chain A residue 1297 CYS Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1846 ASN Chi-restraints excluded: chain A residue 1856 ASP Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 2004 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 65 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1868 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17082 Z= 0.281 Angle : 0.550 8.268 23242 Z= 0.278 Chirality : 0.039 0.167 2602 Planarity : 0.003 0.058 2819 Dihedral : 14.275 175.148 2729 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.02 % Allowed : 16.52 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.01 (0.19), residues: 1975 helix: 1.56 (0.18), residues: 924 sheet: -0.30 (0.39), residues: 188 loop : -1.75 (0.19), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 520 HIS 0.004 0.001 HIS A1091 PHE 0.010 0.001 PHE A 649 TYR 0.011 0.001 TYR A1864 ARG 0.008 0.000 ARG A1869 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 131 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 GLU cc_start: 0.8738 (tp30) cc_final: 0.8445 (tp30) REVERT: A 436 MET cc_start: 0.8508 (mpp) cc_final: 0.8130 (mpp) REVERT: A 777 MET cc_start: 0.8186 (mmm) cc_final: 0.7965 (tpp) REVERT: A 800 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8520 (mm-30) REVERT: A 1270 ASP cc_start: 0.8338 (t70) cc_final: 0.8090 (t0) REVERT: A 1339 MET cc_start: 0.8764 (ptp) cc_final: 0.8379 (pmm) REVERT: A 1396 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8670 (t) REVERT: A 1694 ARG cc_start: 0.8609 (tmm160) cc_final: 0.8064 (tmm160) REVERT: A 1868 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8056 (p0) REVERT: A 1913 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7381 (ttp80) REVERT: A 1924 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7346 (tm-30) REVERT: A 1933 MET cc_start: 0.7755 (tpt) cc_final: 0.7443 (tpt) REVERT: A 2026 MET cc_start: 0.8843 (tpt) cc_final: 0.8409 (tpp) outliers start: 70 outliers final: 52 residues processed: 189 average time/residue: 0.2908 time to fit residues: 85.6497 Evaluate side-chains 183 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 127 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 841 ASN Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1297 CYS Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1600 VAL Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1807 ARG Chi-restraints excluded: chain A residue 1846 ASN Chi-restraints excluded: chain A residue 1856 ASP Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1913 ARG Chi-restraints excluded: chain A residue 2004 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 187 optimal weight: 10.0000 chunk 21 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 chunk 142 optimal weight: 7.9990 chunk 163 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 121 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 HIS ** A1834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1868 ASN A1896 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17082 Z= 0.208 Angle : 0.535 11.770 23242 Z= 0.267 Chirality : 0.038 0.171 2602 Planarity : 0.003 0.057 2819 Dihedral : 14.239 174.446 2729 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.19 % Allowed : 17.04 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.09 (0.19), residues: 1975 helix: 1.64 (0.18), residues: 926 sheet: -0.22 (0.40), residues: 188 loop : -1.73 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1892 HIS 0.013 0.001 HIS A1896 PHE 0.009 0.001 PHE A 911 TYR 0.012 0.001 TYR A1864 ARG 0.004 0.000 ARG A 823 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 130 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.8629 (tpp) cc_final: 0.8335 (tpt) REVERT: A 274 GLU cc_start: 0.8719 (tp30) cc_final: 0.8418 (tp30) REVERT: A 406 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8134 (mt) REVERT: A 523 CYS cc_start: 0.9545 (OUTLIER) cc_final: 0.9139 (t) REVERT: A 710 MET cc_start: 0.9450 (OUTLIER) cc_final: 0.8436 (ttp) REVERT: A 800 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8501 (mm-30) REVERT: A 1270 ASP cc_start: 0.8377 (t70) cc_final: 0.8097 (t0) REVERT: A 1381 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8214 (tt0) REVERT: A 1396 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8716 (t) REVERT: A 1694 ARG cc_start: 0.8609 (tmm160) cc_final: 0.8067 (tmm160) REVERT: A 1868 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.7957 (p0) REVERT: A 1913 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7355 (ttp80) REVERT: A 1924 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7355 (tm-30) REVERT: A 2026 MET cc_start: 0.8853 (tpt) cc_final: 0.8436 (tpp) outliers start: 73 outliers final: 53 residues processed: 190 average time/residue: 0.2984 time to fit residues: 87.5953 Evaluate side-chains 189 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 128 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 841 ASN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1278 MET Chi-restraints excluded: chain A residue 1297 CYS Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1731 ASP Chi-restraints excluded: chain A residue 1807 ARG Chi-restraints excluded: chain A residue 1846 ASN Chi-restraints excluded: chain A residue 1856 ASP Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1896 HIS Chi-restraints excluded: chain A residue 1913 ARG Chi-restraints excluded: chain A residue 1950 THR Chi-restraints excluded: chain A residue 2004 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 77 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 123 optimal weight: 0.5980 chunk 131 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1868 ASN A1896 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17082 Z= 0.207 Angle : 0.538 9.271 23242 Z= 0.268 Chirality : 0.038 0.173 2602 Planarity : 0.003 0.056 2819 Dihedral : 14.221 174.736 2729 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.13 % Allowed : 17.15 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.11 (0.19), residues: 1975 helix: 1.66 (0.18), residues: 924 sheet: -0.22 (0.40), residues: 188 loop : -1.72 (0.19), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 520 HIS 0.018 0.001 HIS A1896 PHE 0.009 0.001 PHE A 911 TYR 0.024 0.001 TYR A1306 ARG 0.004 0.000 ARG A 823 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 130 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.8670 (tpp) cc_final: 0.8384 (tpt) REVERT: A 274 GLU cc_start: 0.8722 (tp30) cc_final: 0.8420 (tp30) REVERT: A 406 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8141 (mt) REVERT: A 523 CYS cc_start: 0.9544 (OUTLIER) cc_final: 0.9161 (t) REVERT: A 710 MET cc_start: 0.9448 (OUTLIER) cc_final: 0.8412 (ttp) REVERT: A 777 MET cc_start: 0.8143 (tpt) cc_final: 0.7795 (tpp) REVERT: A 800 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8514 (mm-30) REVERT: A 1270 ASP cc_start: 0.8382 (t70) cc_final: 0.8130 (t0) REVERT: A 1339 MET cc_start: 0.8712 (ptp) cc_final: 0.8329 (pmm) REVERT: A 1381 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8196 (tt0) REVERT: A 1396 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8693 (t) REVERT: A 1694 ARG cc_start: 0.8610 (tmm160) cc_final: 0.8069 (tmm160) REVERT: A 1913 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7360 (ttp80) REVERT: A 1924 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7334 (tm-30) REVERT: A 2026 MET cc_start: 0.8878 (tpt) cc_final: 0.8324 (tpp) outliers start: 72 outliers final: 57 residues processed: 189 average time/residue: 0.3038 time to fit residues: 89.0371 Evaluate side-chains 192 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 128 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 841 ASN Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1278 MET Chi-restraints excluded: chain A residue 1297 CYS Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1365 ILE Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1601 VAL Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1807 ARG Chi-restraints excluded: chain A residue 1846 ASN Chi-restraints excluded: chain A residue 1856 ASP Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1896 HIS Chi-restraints excluded: chain A residue 1913 ARG Chi-restraints excluded: chain A residue 1950 THR Chi-restraints excluded: chain A residue 1981 ILE Chi-restraints excluded: chain A residue 2004 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 185 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 180 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 163 optimal weight: 10.0000 chunk 170 optimal weight: 0.6980 chunk 179 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1564 HIS ** A1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1896 HIS A1912 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 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 : 0.007 0.093 17082 Z= 0.452 Angle : 0.660 9.541 23242 Z= 0.333 Chirality : 0.042 0.190 2602 Planarity : 0.004 0.062 2819 Dihedral : 14.308 175.729 2729 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.19 % Allowed : 17.73 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.19), residues: 1975 helix: 1.35 (0.17), residues: 915 sheet: -0.47 (0.39), residues: 188 loop : -1.80 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1892 HIS 0.023 0.001 HIS A1896 PHE 0.013 0.002 PHE A 649 TYR 0.033 0.002 TYR A1306 ARG 0.008 0.000 ARG A 823 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 124 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 GLU cc_start: 0.8752 (tp30) cc_final: 0.8454 (tp30) REVERT: A 406 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8076 (mt) REVERT: A 436 MET cc_start: 0.8504 (mpp) cc_final: 0.8187 (mpp) REVERT: A 523 CYS cc_start: 0.9563 (OUTLIER) cc_final: 0.9184 (t) REVERT: A 710 MET cc_start: 0.9457 (OUTLIER) cc_final: 0.8567 (ttp) REVERT: A 777 MET cc_start: 0.8301 (tpt) cc_final: 0.7924 (tpp) REVERT: A 800 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8580 (mm-30) REVERT: A 1270 ASP cc_start: 0.8364 (t70) cc_final: 0.8119 (t0) REVERT: A 1396 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8666 (t) REVERT: A 1694 ARG cc_start: 0.8623 (tmm160) cc_final: 0.8076 (tmm160) REVERT: A 1913 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7303 (ttp80) REVERT: A 1924 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7344 (tm-30) REVERT: A 2026 MET cc_start: 0.8844 (tpt) cc_final: 0.8462 (tpp) outliers start: 73 outliers final: 57 residues processed: 187 average time/residue: 0.2994 time to fit residues: 86.7798 Evaluate side-chains 187 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 124 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 841 ASN Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1297 CYS Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1340 VAL Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1396 THR Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1548 LEU Chi-restraints excluded: chain A residue 1601 VAL Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1807 ARG Chi-restraints excluded: chain A residue 1846 ASN Chi-restraints excluded: chain A residue 1856 ASP Chi-restraints excluded: chain A residue 1868 ASN Chi-restraints excluded: chain A residue 1913 ARG Chi-restraints excluded: chain A residue 1950 THR Chi-restraints excluded: chain A residue 1981 ILE Chi-restraints excluded: chain A residue 2004 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 190 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 200 optimal weight: 20.0000 chunk 184 optimal weight: 30.0000 chunk 159 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1564 HIS ** A1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17082 Z= 0.221 Angle : 0.562 10.020 23242 Z= 0.279 Chirality : 0.038 0.171 2602 Planarity : 0.003 0.059 2819 Dihedral : 14.248 175.201 2729 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.61 % Allowed : 18.59 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.02 (0.19), residues: 1975 helix: 1.60 (0.18), residues: 922 sheet: -0.34 (0.39), residues: 188 loop : -1.80 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 520 HIS 0.003 0.001 HIS A2011 PHE 0.010 0.001 PHE A1634 TYR 0.024 0.001 TYR A1306 ARG 0.008 0.000 ARG A1783 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3950 Ramachandran restraints generated. 1975 Oldfield, 0 Emsley, 1975 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 130 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.8638 (tpp) cc_final: 0.8346 (tpt) REVERT: A 274 GLU cc_start: 0.8730 (tp30) cc_final: 0.8431 (tp30) REVERT: A 406 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8143 (mt) REVERT: A 436 MET cc_start: 0.8491 (mpp) cc_final: 0.8229 (mpp) REVERT: A 523 CYS cc_start: 0.9544 (OUTLIER) cc_final: 0.9160 (t) REVERT: A 710 MET cc_start: 0.9460 (OUTLIER) cc_final: 0.8385 (ttp) REVERT: A 777 MET cc_start: 0.8276 (tpt) cc_final: 0.7911 (tpp) REVERT: A 800 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8549 (mm-30) REVERT: A 1270 ASP cc_start: 0.8368 (t70) cc_final: 0.8100 (t0) REVERT: A 1339 MET cc_start: 0.8784 (ptp) cc_final: 0.8365 (pmm) REVERT: A 1381 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8226 (tt0) REVERT: A 1694 ARG cc_start: 0.8605 (tmm160) cc_final: 0.8071 (tmm160) REVERT: A 1913 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7365 (ttp80) REVERT: A 1924 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7329 (tm-30) REVERT: A 2026 MET cc_start: 0.8870 (tpt) cc_final: 0.8291 (tpp) outliers start: 63 outliers final: 53 residues processed: 182 average time/residue: 0.3402 time to fit residues: 96.0223 Evaluate side-chains 186 residues out of total 1743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 127 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 669 THR Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 800 GLU Chi-restraints excluded: chain A residue 841 ASN Chi-restraints excluded: chain A residue 848 MET Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 987 LYS Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1168 SER Chi-restraints excluded: chain A residue 1173 VAL Chi-restraints excluded: chain A residue 1178 CYS Chi-restraints excluded: chain A residue 1180 GLU Chi-restraints excluded: chain A residue 1195 THR Chi-restraints excluded: chain A residue 1205 ILE Chi-restraints excluded: chain A residue 1208 THR Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1297 CYS Chi-restraints excluded: chain A residue 1338 VAL Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1381 GLU Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1413 VAL Chi-restraints excluded: chain A residue 1467 GLN Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1717 VAL Chi-restraints excluded: chain A residue 1724 VAL Chi-restraints excluded: chain A residue 1807 ARG Chi-restraints excluded: chain A residue 1846 ASN Chi-restraints excluded: chain A residue 1856 ASP Chi-restraints excluded: chain A residue 1913 ARG Chi-restraints excluded: chain A residue 1915 MET Chi-restraints excluded: chain A residue 1950 THR Chi-restraints excluded: chain A residue 1981 ILE Chi-restraints excluded: chain A residue 2004 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 159 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1564 HIS ** A1691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.100105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.072194 restraints weight = 42953.572| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.43 r_work: 0.3031 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17082 Z= 0.292 Angle : 0.593 11.525 23242 Z= 0.294 Chirality : 0.039 0.173 2602 Planarity : 0.003 0.058 2819 Dihedral : 14.231 175.603 2729 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.67 % Allowed : 18.53 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.04 (0.19), residues: 1975 helix: 1.57 (0.18), residues: 918 sheet: -0.37 (0.39), residues: 188 loop : -1.78 (0.19), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1892 HIS 0.004 0.001 HIS A1091 PHE 0.010 0.001 PHE A 649 TYR 0.032 0.001 TYR A1306 ARG 0.007 0.000 ARG A 823 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3699.26 seconds wall clock time: 68 minutes 32.77 seconds (4112.77 seconds total)