Starting phenix.real_space_refine on Fri Feb 23 10:11:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zvw_14989/02_2024/7zvw_14989_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zvw_14989/02_2024/7zvw_14989.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zvw_14989/02_2024/7zvw_14989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zvw_14989/02_2024/7zvw_14989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zvw_14989/02_2024/7zvw_14989_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zvw_14989/02_2024/7zvw_14989_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= 0.005 sd= 0.062 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 6 5.49 5 Mg 2 5.21 5 S 141 5.16 5 C 24175 2.51 5 N 6550 2.21 5 O 7031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 767": "OE1" <-> "OE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A GLU 879": "OE1" <-> "OE2" Residue "A PHE 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1056": "OE1" <-> "OE2" Residue "A TYR 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1481": "OE1" <-> "OE2" Residue "A PHE 1595": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2556": "OE1" <-> "OE2" Residue "A GLU 2578": "OE1" <-> "OE2" Residue "A ASP 2592": "OD1" <-> "OD2" Residue "A GLU 2666": "OE1" <-> "OE2" Residue "A TYR 2696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2750": "OE1" <-> "OE2" Residue "A GLU 2960": "OE1" <-> "OE2" Residue "A PHE 3123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3413": "OE1" <-> "OE2" Residue "A GLU 3551": "OE1" <-> "OE2" Residue "A GLU 3562": "OE1" <-> "OE2" Residue "A GLU 3590": "OE1" <-> "OE2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "G GLU 114": "OE1" <-> "OE2" Residue "G ASP 169": "OD1" <-> "OD2" Residue "G GLU 249": "OE1" <-> "OE2" Residue "E PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 446": "OD1" <-> "OD2" Residue "E GLU 451": "OE1" <-> "OE2" Residue "E GLU 457": "OE1" <-> "OE2" Residue "E PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "F PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 292": "NH1" <-> "NH2" Residue "C GLU 481": "OE1" <-> "OE2" Residue "C PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 37905 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 24052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3226, 24052 Classifications: {'peptide': 3226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 608} Link IDs: {'PTRANS': 127, 'TRANS': 3098} Chain breaks: 38 Unresolved non-hydrogen bonds: 2187 Unresolved non-hydrogen angles: 2792 Unresolved non-hydrogen dihedrals: 1764 Unresolved non-hydrogen chiralities: 235 Planarities with less than four sites: {'GLN:plan1': 34, 'ASP:plan': 34, 'TYR:plan': 24, 'ASN:plan1': 40, 'TRP:plan': 4, 'HIS:plan': 11, 'PHE:plan': 30, 'GLU:plan': 60, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 1177 Chain: "B" Number of atoms: 2735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2735 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 19, 'TRANS': 330} Chain breaks: 2 Chain: "G" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3310 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 22, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3952 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 34, 'TRANS': 453} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1877 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1805 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 16, 'TRANS': 207} Chain breaks: 1 Chain: "H" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.25, per 1000 atoms: 0.51 Number of scatterers: 37905 At special positions: 0 Unit cell: (138.782, 180.158, 233.602, 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 141 16.00 P 6 15.00 Mg 2 11.99 O 7031 8.00 N 6550 7.00 C 24175 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.11 Conformation dependent library (CDL) restraints added in 7.1 seconds 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9558 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 240 helices and 18 sheets defined 61.5% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.46 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 21 through 35 Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.534A pdb=" N ILE A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Proline residue: A 52 - end of helix Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 90 through 107 Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 136 through 157 Proline residue: A 151 - end of helix Processing helix chain 'A' and resid 188 through 203 Processing helix chain 'A' and resid 207 through 223 removed outlier: 3.617A pdb=" N LEU A 210 " --> pdb=" O MET A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 288 Processing helix chain 'A' and resid 298 through 311 Proline residue: A 302 - end of helix Processing helix chain 'A' and resid 317 through 332 removed outlier: 3.503A pdb=" N LEU A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 332 " --> pdb=" O ARG A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 357 through 381 removed outlier: 4.817A pdb=" N ARG A 364 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Proline residue: A 365 - end of helix removed outlier: 6.295A pdb=" N ASP A 380 " --> pdb=" O HIS A 376 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N HIS A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 Processing helix chain 'A' and resid 405 through 424 removed outlier: 3.986A pdb=" N GLU A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 456 removed outlier: 3.611A pdb=" N GLN A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 435 " --> pdb=" O SER A 431 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 452 " --> pdb=" O MET A 448 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASN A 454 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLY A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 544 No H-bonds generated for 'chain 'A' and resid 542 through 544' Processing helix chain 'A' and resid 557 through 582 removed outlier: 3.714A pdb=" N THR A 574 " --> pdb=" O THR A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 624 removed outlier: 4.035A pdb=" N ARG A 623 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N PHE A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 668 Processing helix chain 'A' and resid 672 through 690 Proline residue: A 684 - end of helix Processing helix chain 'A' and resid 694 through 705 removed outlier: 3.504A pdb=" N HIS A 698 " --> pdb=" O SER A 695 " (cutoff:3.500A) Proline residue: A 700 - end of helix Processing helix chain 'A' and resid 707 through 727 removed outlier: 4.226A pdb=" N SER A 711 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N SER A 712 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 715 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL A 726 " --> pdb=" O LYS A 722 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ASP A 727 " --> pdb=" O SER A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 752 removed outlier: 3.701A pdb=" N VAL A 750 " --> pdb=" O CYS A 746 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 751 " --> pdb=" O PHE A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 776 removed outlier: 5.144A pdb=" N SER A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Proline residue: A 763 - end of helix removed outlier: 4.659A pdb=" N ASN A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU A 767 " --> pdb=" O PRO A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 795 Processing helix chain 'A' and resid 799 through 821 removed outlier: 4.036A pdb=" N ASN A 803 " --> pdb=" O GLY A 799 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Proline residue: A 810 - end of helix Processing helix chain 'A' and resid 830 through 840 Processing helix chain 'A' and resid 846 through 850 Processing helix chain 'A' and resid 853 through 864 removed outlier: 3.926A pdb=" N LYS A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Proline residue: A 859 - end of helix removed outlier: 4.155A pdb=" N TYR A 862 " --> pdb=" O LYS A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 884 removed outlier: 3.789A pdb=" N ASP A 883 " --> pdb=" O GLU A 879 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN A 884 " --> pdb=" O LEU A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 908 Proline residue: A 892 - end of helix Proline residue: A 896 - end of helix removed outlier: 5.059A pdb=" N ASP A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ASP A 900 " --> pdb=" O PRO A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 929 Processing helix chain 'A' and resid 974 through 982 removed outlier: 3.672A pdb=" N SER A 979 " --> pdb=" O SER A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1006 Processing helix chain 'A' and resid 1015 through 1028 Processing helix chain 'A' and resid 1031 through 1035 removed outlier: 3.926A pdb=" N GLU A1035 " --> pdb=" O ILE A1031 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1031 through 1035' Processing helix chain 'A' and resid 1048 through 1070 removed outlier: 3.740A pdb=" N VAL A1069 " --> pdb=" O ILE A1065 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N SER A1070 " --> pdb=" O PHE A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1098 Processing helix chain 'A' and resid 1124 through 1133 Processing helix chain 'A' and resid 1137 through 1158 Processing helix chain 'A' and resid 1161 through 1167 removed outlier: 4.018A pdb=" N LYS A1166 " --> pdb=" O ASP A1162 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE A1167 " --> pdb=" O CYS A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1182 removed outlier: 3.641A pdb=" N PHE A1182 " --> pdb=" O ILE A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1201 Processing helix chain 'A' and resid 1207 through 1212 Processing helix chain 'A' and resid 1214 through 1227 Processing helix chain 'A' and resid 1235 through 1250 removed outlier: 4.199A pdb=" N LYS A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1261 No H-bonds generated for 'chain 'A' and resid 1258 through 1261' Processing helix chain 'A' and resid 1264 through 1276 Processing helix chain 'A' and resid 1281 through 1297 Processing helix chain 'A' and resid 1302 through 1307 Processing helix chain 'A' and resid 1311 through 1318 Proline residue: A1316 - end of helix Processing helix chain 'A' and resid 1327 through 1341 Processing helix chain 'A' and resid 1352 through 1363 Processing helix chain 'A' and resid 1383 through 1403 Processing helix chain 'A' and resid 1405 through 1411 removed outlier: 3.546A pdb=" N ALA A1410 " --> pdb=" O GLU A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1428 Processing helix chain 'A' and resid 1433 through 1447 Processing helix chain 'A' and resid 1455 through 1470 Proline residue: A1464 - end of helix Processing helix chain 'A' and resid 1477 through 1488 Processing helix chain 'A' and resid 1496 through 1510 Processing helix chain 'A' and resid 1514 through 1519 Processing helix chain 'A' and resid 1527 through 1539 removed outlier: 4.046A pdb=" N PHE A1539 " --> pdb=" O ILE A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1550 through 1563 Processing helix chain 'A' and resid 1571 through 1582 removed outlier: 3.694A pdb=" N GLU A1574 " --> pdb=" O PRO A1571 " (cutoff:3.500A) Proline residue: A1575 - end of helix removed outlier: 4.027A pdb=" N LYS A1578 " --> pdb=" O PRO A1575 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A1582 " --> pdb=" O PHE A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1592 Processing helix chain 'A' and resid 1598 through 1609 removed outlier: 3.617A pdb=" N ARG A1603 " --> pdb=" O GLU A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1614 through 1632 Proline residue: A1625 - end of helix removed outlier: 4.088A pdb=" N ARG A1628 " --> pdb=" O LEU A1624 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY A1629 " --> pdb=" O PRO A1625 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A1630 " --> pdb=" O ARG A1626 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A1631 " --> pdb=" O VAL A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1657 Processing helix chain 'A' and resid 1659 through 1664 removed outlier: 3.899A pdb=" N ILE A1662 " --> pdb=" O LYS A1659 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A1663 " --> pdb=" O GLU A1660 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP A1664 " --> pdb=" O TRP A1661 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1659 through 1664' Processing helix chain 'A' and resid 1666 through 1683 Processing helix chain 'A' and resid 1694 through 1713 Processing helix chain 'A' and resid 1718 through 1728 removed outlier: 3.919A pdb=" N ILE A1728 " --> pdb=" O PHE A1724 " (cutoff:3.500A) Processing helix chain 'A' and resid 1736 through 1747 removed outlier: 3.753A pdb=" N ASP A1740 " --> pdb=" O VAL A1736 " (cutoff:3.500A) Processing helix chain 'A' and resid 1754 through 1765 Processing helix chain 'A' and resid 1774 through 1793 Proline residue: A1786 - end of helix Processing helix chain 'A' and resid 1812 through 1819 removed outlier: 4.262A pdb=" N SER A1818 " --> pdb=" O LYS A1814 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1830 Proline residue: A1826 - end of helix removed outlier: 3.577A pdb=" N ASP A1829 " --> pdb=" O PRO A1826 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1853 Processing helix chain 'A' and resid 1860 through 1874 Processing helix chain 'A' and resid 1878 through 1894 Processing helix chain 'A' and resid 1902 through 1909 Processing helix chain 'A' and resid 1915 through 1929 removed outlier: 3.945A pdb=" N LEU A1920 " --> pdb=" O ASP A1916 " (cutoff:3.500A) Processing helix chain 'A' and resid 1944 through 1951 Processing helix chain 'A' and resid 1959 through 1974 Proline residue: A1971 - end of helix removed outlier: 5.345A pdb=" N PHE A1974 " --> pdb=" O PHE A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1979 through 1993 Proline residue: A1983 - end of helix Processing helix chain 'A' and resid 2001 through 2020 Processing helix chain 'A' and resid 2086 through 2101 Processing helix chain 'A' and resid 2111 through 2124 Processing helix chain 'A' and resid 2135 through 2139 Processing helix chain 'A' and resid 2153 through 2167 Processing helix chain 'A' and resid 2174 through 2187 removed outlier: 4.616A pdb=" N GLN A2183 " --> pdb=" O VAL A2179 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LYS A2184 " --> pdb=" O SER A2180 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A2185 " --> pdb=" O TYR A2181 " (cutoff:3.500A) Processing helix chain 'A' and resid 2196 through 2213 Processing helix chain 'A' and resid 2222 through 2238 Processing helix chain 'A' and resid 2249 through 2261 Processing helix chain 'A' and resid 2273 through 2285 Processing helix chain 'A' and resid 2304 through 2311 Processing helix chain 'A' and resid 2313 through 2321 removed outlier: 4.808A pdb=" N LEU A2319 " --> pdb=" O LYS A2315 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N CYS A2320 " --> pdb=" O ILE A2316 " (cutoff:3.500A) Processing helix chain 'A' and resid 2330 through 2343 Processing helix chain 'A' and resid 2348 through 2362 Processing helix chain 'A' and resid 2371 through 2385 Processing helix chain 'A' and resid 2392 through 2406 Processing helix chain 'A' and resid 2412 through 2427 Processing helix chain 'A' and resid 2431 through 2444 Processing helix chain 'A' and resid 2449 through 2458 Processing helix chain 'A' and resid 2471 through 2481 removed outlier: 4.195A pdb=" N SER A2481 " --> pdb=" O LEU A2477 " (cutoff:3.500A) Processing helix chain 'A' and resid 2522 through 2535 Processing helix chain 'A' and resid 2540 through 2550 removed outlier: 5.448A pdb=" N ASN A2545 " --> pdb=" O ASP A2542 " (cutoff:3.500A) Proline residue: A2546 - end of helix Processing helix chain 'A' and resid 2555 through 2571 Proline residue: A2567 - end of helix Processing helix chain 'A' and resid 2575 through 2590 removed outlier: 3.572A pdb=" N GLU A2578 " --> pdb=" O SER A2575 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LEU A2579 " --> pdb=" O ARG A2576 " (cutoff:3.500A) Processing helix chain 'A' and resid 2592 through 2597 removed outlier: 3.781A pdb=" N ARG A2596 " --> pdb=" O TYR A2593 " (cutoff:3.500A) Processing helix chain 'A' and resid 2604 through 2614 Processing helix chain 'A' and resid 2622 through 2631 Processing helix chain 'A' and resid 2635 through 2646 removed outlier: 3.944A pdb=" N LEU A2645 " --> pdb=" O LEU A2641 " (cutoff:3.500A) Processing helix chain 'A' and resid 2651 through 2670 removed outlier: 4.743A pdb=" N LYS A2655 " --> pdb=" O ASP A2652 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A2656 " --> pdb=" O ASN A2653 " (cutoff:3.500A) Processing helix chain 'A' and resid 2674 through 2684 Processing helix chain 'A' and resid 2688 through 2699 Processing helix chain 'A' and resid 2703 through 2717 Processing helix chain 'A' and resid 2728 through 2741 Processing helix chain 'A' and resid 2745 through 2755 removed outlier: 4.120A pdb=" N GLU A2750 " --> pdb=" O GLU A2746 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A2751 " --> pdb=" O ILE A2747 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 Processing helix chain 'A' and resid 2775 through 2785 Processing helix chain 'A' and resid 2791 through 2806 Processing helix chain 'A' and resid 2812 through 2832 Processing helix chain 'A' and resid 2839 through 2865 removed outlier: 3.503A pdb=" N GLY A2843 " --> pdb=" O ALA A2840 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU A2853 " --> pdb=" O GLN A2850 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A2865 " --> pdb=" O SER A2862 " (cutoff:3.500A) Processing helix chain 'A' and resid 2872 through 2888 removed outlier: 4.097A pdb=" N GLN A2877 " --> pdb=" O ASP A2873 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU A2878 " --> pdb=" O VAL A2874 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A2888 " --> pdb=" O GLN A2884 " (cutoff:3.500A) Processing helix chain 'A' and resid 2897 through 2917 Processing helix chain 'A' and resid 2943 through 2958 Processing helix chain 'A' and resid 2963 through 2973 Processing helix chain 'A' and resid 2980 through 2996 Processing helix chain 'A' and resid 2998 through 3003 Processing helix chain 'A' and resid 3005 through 3008 No H-bonds generated for 'chain 'A' and resid 3005 through 3008' Processing helix chain 'A' and resid 3018 through 3034 Processing helix chain 'A' and resid 3038 through 3051 Processing helix chain 'A' and resid 3056 through 3072 Processing helix chain 'A' and resid 3079 through 3091 removed outlier: 4.051A pdb=" N ILE A3084 " --> pdb=" O LYS A3081 " (cutoff:3.500A) Processing helix chain 'A' and resid 3100 through 3111 Processing helix chain 'A' and resid 3118 through 3125 Processing helix chain 'A' and resid 3133 through 3135 No H-bonds generated for 'chain 'A' and resid 3133 through 3135' Processing helix chain 'A' and resid 3137 through 3147 Proline residue: A3140 - end of helix Processing helix chain 'A' and resid 3149 through 3164 removed outlier: 4.432A pdb=" N LYS A3152 " --> pdb=" O LYS A3149 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG A3155 " --> pdb=" O LYS A3152 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS A3156 " --> pdb=" O ILE A3153 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A3163 " --> pdb=" O GLN A3160 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER A3164 " --> pdb=" O ILE A3161 " (cutoff:3.500A) Processing helix chain 'A' and resid 3166 through 3175 removed outlier: 3.762A pdb=" N PHE A3171 " --> pdb=" O GLN A3167 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLN A3172 " --> pdb=" O SER A3168 " (cutoff:3.500A) Processing helix chain 'A' and resid 3282 through 3295 removed outlier: 3.906A pdb=" N VAL A3286 " --> pdb=" O PRO A3282 " (cutoff:3.500A) Processing helix chain 'A' and resid 3298 through 3314 Processing helix chain 'A' and resid 3319 through 3340 Processing helix chain 'A' and resid 3352 through 3364 Processing helix chain 'A' and resid 3369 through 3379 Processing helix chain 'A' and resid 3385 through 3405 Processing helix chain 'A' and resid 3412 through 3415 No H-bonds generated for 'chain 'A' and resid 3412 through 3415' Processing helix chain 'A' and resid 3417 through 3420 No H-bonds generated for 'chain 'A' and resid 3417 through 3420' Processing helix chain 'A' and resid 3422 through 3425 No H-bonds generated for 'chain 'A' and resid 3422 through 3425' Processing helix chain 'A' and resid 3435 through 3437 No H-bonds generated for 'chain 'A' and resid 3435 through 3437' Processing helix chain 'A' and resid 3491 through 3508 Processing helix chain 'A' and resid 3512 through 3517 removed outlier: 4.264A pdb=" N ARG A3517 " --> pdb=" O GLN A3513 " (cutoff:3.500A) Processing helix chain 'A' and resid 3545 through 3556 Processing helix chain 'A' and resid 3560 through 3574 Proline residue: A3563 - end of helix removed outlier: 3.531A pdb=" N ALA A3574 " --> pdb=" O LEU A3571 " (cutoff:3.500A) Processing helix chain 'A' and resid 3584 through 3598 Processing helix chain 'A' and resid 3605 through 3612 Processing helix chain 'A' and resid 3616 through 3639 Processing helix chain 'A' and resid 3671 through 3673 No H-bonds generated for 'chain 'A' and resid 3671 through 3673' Processing helix chain 'A' and resid 3678 through 3680 No H-bonds generated for 'chain 'A' and resid 3678 through 3680' Processing helix chain 'A' and resid 3707 through 3713 Processing helix chain 'A' and resid 3717 through 3720 No H-bonds generated for 'chain 'A' and resid 3717 through 3720' Processing helix chain 'A' and resid 3722 through 3732 Processing helix chain 'A' and resid 3740 through 3758 removed outlier: 4.083A pdb=" N SER A3745 " --> pdb=" O GLU A3741 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU A3746 " --> pdb=" O GLN A3742 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE A3747 " --> pdb=" O TYR A3743 " (cutoff:3.500A) Processing helix chain 'A' and resid 3766 through 3787 removed outlier: 4.075A pdb=" N LEU A3787 " --> pdb=" O ARG A3783 " (cutoff:3.500A) Processing helix chain 'A' and resid 3799 through 3809 Processing helix chain 'A' and resid 3811 through 3815 Processing helix chain 'A' and resid 3819 through 3821 No H-bonds generated for 'chain 'A' and resid 3819 through 3821' Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 80 through 92 removed outlier: 4.304A pdb=" N LYS B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 138 through 147 removed outlier: 4.798A pdb=" N SER B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLY B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 175 No H-bonds generated for 'chain 'B' and resid 173 through 175' Processing helix chain 'B' and resid 183 through 197 Processing helix chain 'B' and resid 204 through 216 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.610A pdb=" N ALA B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.520A pdb=" N LEU B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 254 through 263' Processing helix chain 'B' and resid 275 through 285 Processing helix chain 'B' and resid 288 through 296 removed outlier: 4.223A pdb=" N LYS B 292 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 296 " --> pdb=" O LYS B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 336 through 349 removed outlier: 5.778A pdb=" N VAL B 340 " --> pdb=" O LYS B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 356 Processing helix chain 'B' and resid 360 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.590A pdb=" N HIS B 372 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 374 " --> pdb=" O VAL B 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 62 removed outlier: 3.972A pdb=" N LEU G 62 " --> pdb=" O GLU G 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 58 through 62' Processing helix chain 'G' and resid 82 through 95 removed outlier: 3.583A pdb=" N LYS G 87 " --> pdb=" O GLU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 127 Processing helix chain 'G' and resid 139 through 147 Processing helix chain 'G' and resid 174 through 176 No H-bonds generated for 'chain 'G' and resid 174 through 176' Processing helix chain 'G' and resid 184 through 198 Processing helix chain 'G' and resid 233 through 251 removed outlier: 3.647A pdb=" N ARG G 242 " --> pdb=" O PHE G 238 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE G 243 " --> pdb=" O HIS G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 269 removed outlier: 4.328A pdb=" N GLU G 267 " --> pdb=" O LEU G 263 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR G 268 " --> pdb=" O LYS G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 297 removed outlier: 4.388A pdb=" N LEU G 297 " --> pdb=" O LEU G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 374 Processing helix chain 'G' and resid 380 through 385 Processing helix chain 'G' and resid 392 through 395 Processing helix chain 'G' and resid 399 through 410 Processing helix chain 'G' and resid 424 through 428 Processing helix chain 'G' and resid 430 through 440 Processing helix chain 'G' and resid 443 through 447 Processing helix chain 'G' and resid 451 through 457 Processing helix chain 'G' and resid 460 through 466 Processing helix chain 'E' and resid 167 through 173 Processing helix chain 'E' and resid 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'E' and resid 220 through 228 Processing helix chain 'E' and resid 232 through 238 Proline residue: E 237 - end of helix Processing helix chain 'E' and resid 245 through 269 Processing helix chain 'E' and resid 292 through 331 Processing helix chain 'E' and resid 333 through 335 No H-bonds generated for 'chain 'E' and resid 333 through 335' Processing helix chain 'E' and resid 347 through 352 Processing helix chain 'E' and resid 429 through 431 No H-bonds generated for 'chain 'E' and resid 429 through 431' Processing helix chain 'E' and resid 448 through 450 No H-bonds generated for 'chain 'E' and resid 448 through 450' Processing helix chain 'E' and resid 453 through 458 Processing helix chain 'E' and resid 478 through 481 No H-bonds generated for 'chain 'E' and resid 478 through 481' Processing helix chain 'E' and resid 508 through 511 No H-bonds generated for 'chain 'E' and resid 508 through 511' Processing helix chain 'E' and resid 555 through 567 Processing helix chain 'E' and resid 572 through 579 Processing helix chain 'E' and resid 596 through 607 Processing helix chain 'E' and resid 620 through 636 Processing helix chain 'E' and resid 656 through 685 removed outlier: 3.654A pdb=" N ARG E 659 " --> pdb=" O ARG E 656 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N TRP E 660 " --> pdb=" O ARG E 657 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY E 661 " --> pdb=" O LEU E 658 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG E 679 " --> pdb=" O ASN E 676 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER E 680 " --> pdb=" O ILE E 677 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL E 683 " --> pdb=" O SER E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 699 through 712 Processing helix chain 'F' and resid 100 through 102 No H-bonds generated for 'chain 'F' and resid 100 through 102' Processing helix chain 'F' and resid 125 through 128 Processing helix chain 'F' and resid 241 through 253 Processing helix chain 'F' and resid 258 through 264 Processing helix chain 'F' and resid 273 through 291 Processing helix chain 'F' and resid 299 through 307 Processing helix chain 'F' and resid 312 through 326 Processing helix chain 'F' and resid 330 through 364 removed outlier: 4.081A pdb=" N ALA F 349 " --> pdb=" O LYS F 345 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA F 350 " --> pdb=" O PHE F 346 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LYS F 351 " --> pdb=" O GLU F 347 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LYS F 352 " --> pdb=" O LEU F 348 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET F 353 " --> pdb=" O ALA F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 392 Processing helix chain 'C' and resid 430 through 456 removed outlier: 3.524A pdb=" N SER C 455 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP C 456 " --> pdb=" O LYS C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 494 removed outlier: 3.721A pdb=" N LEU C 494 " --> pdb=" O ILE C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 511 Processing helix chain 'C' and resid 610 through 619 Processing helix chain 'C' and resid 637 through 639 No H-bonds generated for 'chain 'C' and resid 637 through 639' Processing helix chain 'C' and resid 643 through 664 Processing helix chain 'H' and resid 402 through 406 removed outlier: 3.557A pdb=" N LEU H 406 " --> pdb=" O VAL H 403 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 954 through 957 Processing sheet with id= B, first strand: chain 'A' and resid 3409 through 3411 removed outlier: 6.795A pdb=" N THR A3455 " --> pdb=" O THR A3470 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N THR A3470 " --> pdb=" O THR A3455 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A3467 " --> pdb=" O VAL A3483 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A3534 " --> pdb=" O GLN A3484 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE A3535 " --> pdb=" O PRO A3528 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 3650 through 3652 Processing sheet with id= D, first strand: chain 'A' and resid 3668 through 3670 Processing sheet with id= E, first strand: chain 'A' and resid 3449 through 3452 removed outlier: 7.141A pdb=" N ARG A3472 " --> pdb=" O GLU A3450 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 133 through 137 removed outlier: 7.191A pdb=" N VAL B 104 " --> pdb=" O TYR B 134 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N SER B 136 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU B 106 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU B 9 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N THR B 107 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ILE B 11 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL B 10 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 32 " --> pdb=" O CYS B 18 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 20 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 35 through 38 removed outlier: 3.887A pdb=" N ARG B 38 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR B 67 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 151 through 153 removed outlier: 3.616A pdb=" N ILE B 166 " --> pdb=" O GLY B 151 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B 153 " --> pdb=" O VAL B 164 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 161 through 163 Processing sheet with id= J, first strand: chain 'B' and resid 239 through 242 Processing sheet with id= K, first strand: chain 'G' and resid 16 through 18 removed outlier: 3.511A pdb=" N ILE G 137 " --> pdb=" O VAL G 107 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU G 109 " --> pdb=" O ILE G 137 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 24 through 27 removed outlier: 3.575A pdb=" N LEU G 37 " --> pdb=" O ILE G 27 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 42 through 46 Processing sheet with id= N, first strand: chain 'G' and resid 387 through 389 removed outlier: 6.004A pdb=" N LEU G 153 " --> pdb=" O ILE G 388 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL G 154 " --> pdb=" O THR G 165 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 273 through 276 removed outlier: 3.530A pdb=" N VAL G 283 " --> pdb=" O PHE G 275 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 208 through 211 removed outlier: 6.765A pdb=" N GLU G 223 " --> pdb=" O LYS G 209 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 201 through 207 Processing sheet with id= R, first strand: chain 'F' and resid 74 through 77 1990 hydrogen bonds defined for protein. 5310 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.66 Time building geometry restraints manager: 17.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6341 1.31 - 1.43: 9900 1.43 - 1.56: 22175 1.56 - 1.69: 10 1.69 - 1.82: 228 Bond restraints: 38654 Sorted by residual: bond pdb=" CA SER F 309 " pdb=" CB SER F 309 " ideal model delta sigma weight residual 1.522 1.456 0.066 1.32e-02 5.74e+03 2.52e+01 bond pdb=" C ASN G 14 " pdb=" O ASN G 14 " ideal model delta sigma weight residual 1.235 1.177 0.058 1.26e-02 6.30e+03 2.13e+01 bond pdb=" N THR E 330 " pdb=" CA THR E 330 " ideal model delta sigma weight residual 1.459 1.516 -0.057 1.28e-02 6.10e+03 1.99e+01 bond pdb=" N PRO F 107 " pdb=" CA PRO F 107 " ideal model delta sigma weight residual 1.469 1.412 0.056 1.28e-02 6.10e+03 1.95e+01 bond pdb=" CA SER F 301 " pdb=" CB SER F 301 " ideal model delta sigma weight residual 1.528 1.466 0.062 1.59e-02 3.96e+03 1.53e+01 ... (remaining 38649 not shown) Histogram of bond angle deviations from ideal: 92.21 - 101.74: 88 101.74 - 111.27: 16567 111.27 - 120.80: 24596 120.80 - 130.33: 11080 130.33 - 139.85: 166 Bond angle restraints: 52497 Sorted by residual: angle pdb=" CA PHE F 310 " pdb=" CB PHE F 310 " pdb=" CG PHE F 310 " ideal model delta sigma weight residual 113.80 124.12 -10.32 1.00e+00 1.00e+00 1.07e+02 angle pdb=" CA GLY E 332 " pdb=" C GLY E 332 " pdb=" O GLY E 332 " ideal model delta sigma weight residual 122.52 114.58 7.94 7.90e-01 1.60e+00 1.01e+02 angle pdb=" N GLU F 101 " pdb=" CA GLU F 101 " pdb=" C GLU F 101 " ideal model delta sigma weight residual 112.54 100.37 12.17 1.22e+00 6.72e-01 9.96e+01 angle pdb=" N PRO E 412 " pdb=" CA PRO E 412 " pdb=" CB PRO E 412 " ideal model delta sigma weight residual 103.25 113.10 -9.85 1.05e+00 9.07e-01 8.81e+01 angle pdb=" N GLU H 396 " pdb=" CA GLU H 396 " pdb=" C GLU H 396 " ideal model delta sigma weight residual 111.28 101.65 9.63 1.09e+00 8.42e-01 7.80e+01 ... (remaining 52492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 21111 17.90 - 35.80: 1920 35.80 - 53.70: 346 53.70 - 71.59: 72 71.59 - 89.49: 44 Dihedral angle restraints: 23493 sinusoidal: 8877 harmonic: 14616 Sorted by residual: dihedral pdb=" N ALA G 10 " pdb=" C ALA G 10 " pdb=" CA ALA G 10 " pdb=" CB ALA G 10 " ideal model delta harmonic sigma weight residual 122.90 106.51 16.39 0 2.50e+00 1.60e-01 4.30e+01 dihedral pdb=" N PHE F 310 " pdb=" C PHE F 310 " pdb=" CA PHE F 310 " pdb=" CB PHE F 310 " ideal model delta harmonic sigma weight residual 122.80 108.19 14.61 0 2.50e+00 1.60e-01 3.42e+01 dihedral pdb=" CA GLN A1511 " pdb=" C GLN A1511 " pdb=" N PRO A1512 " pdb=" CA PRO A1512 " ideal model delta harmonic sigma weight residual -180.00 -151.80 -28.20 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 23490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 5708 0.093 - 0.186: 278 0.186 - 0.279: 31 0.279 - 0.372: 14 0.372 - 0.464: 5 Chirality restraints: 6036 Sorted by residual: chirality pdb=" CA GLN H 391 " pdb=" N GLN H 391 " pdb=" C GLN H 391 " pdb=" CB GLN H 391 " both_signs ideal model delta sigma weight residual False 2.51 2.97 -0.46 2.00e-01 2.50e+01 5.39e+00 chirality pdb=" CA PHE F 310 " pdb=" N PHE F 310 " pdb=" C PHE F 310 " pdb=" CB PHE F 310 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" CA ASP E 414 " pdb=" N ASP E 414 " pdb=" C ASP E 414 " pdb=" CB ASP E 414 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 6033 not shown) Planarity restraints: 6755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET E 300 " 0.030 2.00e-02 2.50e+03 5.93e-02 3.52e+01 pdb=" C MET E 300 " -0.103 2.00e-02 2.50e+03 pdb=" O MET E 300 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS E 301 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP E 329 " 0.026 2.00e-02 2.50e+03 4.96e-02 2.46e+01 pdb=" C TRP E 329 " -0.086 2.00e-02 2.50e+03 pdb=" O TRP E 329 " 0.032 2.00e-02 2.50e+03 pdb=" N THR E 330 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 87 " -0.034 2.00e-02 2.50e+03 2.80e-02 1.96e+01 pdb=" CG TRP B 87 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP B 87 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP B 87 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 87 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 87 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 87 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 87 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 87 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 87 " -0.003 2.00e-02 2.50e+03 ... (remaining 6752 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 352 2.58 - 3.16: 33268 3.16 - 3.74: 61714 3.74 - 4.32: 76786 4.32 - 4.90: 126407 Nonbonded interactions: 298527 Sorted by model distance: nonbonded pdb=" O2B ATP G 501 " pdb="MG MG G 502 " model vdw 2.004 2.170 nonbonded pdb=" O3G ATP B 401 " pdb="MG MG B 402 " model vdw 2.093 2.170 nonbonded pdb=" O1B ATP B 401 " pdb="MG MG B 402 " model vdw 2.096 2.170 nonbonded pdb=" OG SER G 22 " pdb="MG MG G 502 " model vdw 2.105 2.170 nonbonded pdb=" O3B ATP G 501 " pdb="MG MG G 502 " model vdw 2.123 2.170 ... (remaining 298522 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: 4.760 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: 0.040 Extract box with map and model: 20.120 Check model and map are aligned: 0.590 Set scattering table: 0.350 Process input model: 104.790 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 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 : 0.004 0.066 38654 Z= 0.241 Angle : 0.752 17.385 52497 Z= 0.450 Chirality : 0.049 0.464 6036 Planarity : 0.005 0.105 6755 Dihedral : 14.633 89.492 13935 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.73 % Favored : 96.06 % Rotamer: Outliers : 0.82 % Allowed : 0.90 % Favored : 98.29 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.13), residues: 4851 helix: 2.18 (0.10), residues: 3035 sheet: -0.62 (0.37), residues: 202 loop : -0.62 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP B 87 HIS 0.007 0.001 HIS G 445 PHE 0.043 0.001 PHE F 79 TYR 0.033 0.001 TYR F 291 ARG 0.008 0.000 ARG F 292 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 4459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1447 time to evaluate : 4.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 MET cc_start: 0.7882 (ppp) cc_final: 0.7265 (ppp) REVERT: A 418 LEU cc_start: 0.9100 (mp) cc_final: 0.8687 (mp) REVERT: A 436 MET cc_start: 0.8533 (mmp) cc_final: 0.8290 (tpp) REVERT: A 440 ASP cc_start: 0.8037 (t0) cc_final: 0.7490 (t0) REVERT: A 572 LEU cc_start: 0.8736 (mt) cc_final: 0.8380 (mt) REVERT: A 612 LYS cc_start: 0.8765 (tttt) cc_final: 0.8450 (tttt) REVERT: A 656 GLU cc_start: 0.6221 (mm-30) cc_final: 0.5602 (mt-10) REVERT: A 666 MET cc_start: 0.7438 (ptm) cc_final: 0.6094 (ptm) REVERT: A 677 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7356 (tt0) REVERT: A 681 GLU cc_start: 0.7809 (mt-10) cc_final: 0.6902 (mt-10) REVERT: A 693 PHE cc_start: 0.7013 (m-80) cc_final: 0.5860 (m-80) REVERT: A 747 PHE cc_start: 0.6955 (m-10) cc_final: 0.6511 (m-80) REVERT: A 792 LEU cc_start: 0.8538 (tp) cc_final: 0.8219 (tp) REVERT: A 795 SER cc_start: 0.7913 (m) cc_final: 0.7457 (t) REVERT: A 888 GLU cc_start: 0.6785 (pm20) cc_final: 0.6523 (pm20) REVERT: A 912 LEU cc_start: 0.5732 (tp) cc_final: 0.5389 (tt) REVERT: A 925 ILE cc_start: 0.6930 (mm) cc_final: 0.6599 (mm) REVERT: A 926 LEU cc_start: 0.7335 (mt) cc_final: 0.6943 (mt) REVERT: A 971 THR cc_start: 0.8142 (p) cc_final: 0.7769 (t) REVERT: A 1023 MET cc_start: 0.8557 (ptp) cc_final: 0.8071 (mtp) REVERT: A 1170 LEU cc_start: 0.8704 (mm) cc_final: 0.8457 (mp) REVERT: A 1248 LEU cc_start: 0.6412 (tp) cc_final: 0.6139 (tp) REVERT: A 1416 ILE cc_start: 0.6244 (mm) cc_final: 0.5773 (mt) REVERT: A 1417 ARG cc_start: 0.7438 (ptm-80) cc_final: 0.6867 (ptp90) REVERT: A 1554 MET cc_start: 0.7626 (tpp) cc_final: 0.7160 (tmm) REVERT: A 1588 PHE cc_start: 0.8618 (t80) cc_final: 0.8308 (t80) REVERT: A 1594 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8595 (tp30) REVERT: A 1738 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7484 (mm-30) REVERT: A 1766 MET cc_start: 0.8487 (ppp) cc_final: 0.8219 (ppp) REVERT: A 1773 LEU cc_start: 0.8524 (mm) cc_final: 0.8216 (mp) REVERT: A 1819 ASP cc_start: 0.7967 (m-30) cc_final: 0.7668 (p0) REVERT: A 1840 ARG cc_start: 0.8227 (mtt-85) cc_final: 0.7789 (mmt180) REVERT: A 1843 LEU cc_start: 0.7839 (mt) cc_final: 0.7515 (mt) REVERT: A 1851 ILE cc_start: 0.8347 (mt) cc_final: 0.7839 (tt) REVERT: A 1872 TYR cc_start: 0.7569 (m-80) cc_final: 0.6985 (m-80) REVERT: A 1888 THR cc_start: 0.6757 (m) cc_final: 0.6162 (p) REVERT: A 1974 PHE cc_start: 0.8411 (m-80) cc_final: 0.8185 (m-80) REVERT: A 2428 LEU cc_start: 0.6629 (mt) cc_final: 0.6376 (mt) REVERT: A 2459 ASP cc_start: 0.7718 (m-30) cc_final: 0.7313 (m-30) REVERT: A 2589 LEU cc_start: 0.6738 (mt) cc_final: 0.6452 (mt) REVERT: A 2673 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6614 (mm-30) REVERT: A 2675 ASP cc_start: 0.7328 (m-30) cc_final: 0.7045 (m-30) REVERT: A 2862 SER cc_start: 0.7628 (t) cc_final: 0.7037 (p) REVERT: A 2902 ASP cc_start: 0.7184 (t70) cc_final: 0.6864 (t0) REVERT: A 2958 LYS cc_start: 0.7201 (mmtt) cc_final: 0.6778 (mmtt) REVERT: A 2963 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7193 (tm-30) REVERT: A 3138 PHE cc_start: 0.6172 (m-10) cc_final: 0.5880 (m-80) REVERT: A 3500 LEU cc_start: 0.7537 (tp) cc_final: 0.7217 (tt) REVERT: A 3562 GLU cc_start: 0.7325 (tp30) cc_final: 0.7099 (tp30) REVERT: A 3614 SER cc_start: 0.7120 (t) cc_final: 0.6911 (p) REVERT: A 3622 PHE cc_start: 0.7483 (t80) cc_final: 0.7018 (t80) REVERT: A 3624 LYS cc_start: 0.7181 (tttp) cc_final: 0.6754 (mtpp) REVERT: A 3726 ILE cc_start: 0.7053 (mt) cc_final: 0.6641 (mt) REVERT: B 84 GLU cc_start: 0.7449 (pp20) cc_final: 0.7179 (tm-30) REVERT: B 108 GLU cc_start: 0.7383 (pp20) cc_final: 0.6680 (pp20) REVERT: B 213 ILE cc_start: 0.7934 (mt) cc_final: 0.7708 (mt) REVERT: B 297 ASN cc_start: 0.8398 (m-40) cc_final: 0.8023 (m-40) REVERT: B 300 MET cc_start: 0.6930 (tmm) cc_final: 0.6573 (tmm) REVERT: B 306 MET cc_start: 0.6516 (ppp) cc_final: 0.6120 (ppp) REVERT: B 314 MET cc_start: 0.8072 (tpt) cc_final: 0.7526 (tpp) REVERT: B 318 LEU cc_start: 0.8524 (tt) cc_final: 0.8084 (mm) REVERT: B 362 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7795 (mm-30) REVERT: G 115 TYR cc_start: 0.6588 (t80) cc_final: 0.6340 (t80) REVERT: G 246 GLU cc_start: 0.6947 (mp0) cc_final: 0.6425 (mp0) REVERT: G 285 PHE cc_start: 0.8296 (m-80) cc_final: 0.8048 (m-80) REVERT: G 390 THR cc_start: 0.8344 (m) cc_final: 0.7912 (t) REVERT: G 403 LEU cc_start: 0.8584 (tp) cc_final: 0.8015 (tp) REVERT: E 200 LYS cc_start: 0.8162 (mttt) cc_final: 0.7326 (mttt) REVERT: E 236 LEU cc_start: 0.8133 (mt) cc_final: 0.7907 (mt) REVERT: E 349 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7735 (mt-10) REVERT: E 519 GLN cc_start: 0.6963 (tt0) cc_final: 0.6308 (tm-30) REVERT: E 523 PHE cc_start: 0.6315 (p90) cc_final: 0.3749 (m-10) REVERT: F 77 VAL cc_start: 0.8864 (m) cc_final: 0.8573 (m) REVERT: F 266 GLU cc_start: 0.7928 (pm20) cc_final: 0.7492 (pm20) REVERT: F 272 MET cc_start: 0.7006 (tmm) cc_final: 0.6524 (tmm) REVERT: F 307 LEU cc_start: 0.9220 (tp) cc_final: 0.9015 (tp) REVERT: F 333 ILE cc_start: 0.8509 (tt) cc_final: 0.8167 (tp) REVERT: C 419 MET cc_start: 0.1135 (ttt) cc_final: 0.0917 (ttt) REVERT: C 429 THR cc_start: 0.5999 (t) cc_final: 0.5686 (m) REVERT: C 451 GLN cc_start: 0.7417 (tt0) cc_final: 0.7069 (tt0) REVERT: C 504 ASP cc_start: 0.7947 (t0) cc_final: 0.7496 (t0) REVERT: C 511 ILE cc_start: 0.8331 (mm) cc_final: 0.8111 (mm) REVERT: C 617 LEU cc_start: 0.8072 (mt) cc_final: 0.7832 (mt) outliers start: 31 outliers final: 8 residues processed: 1464 average time/residue: 0.5567 time to fit residues: 1288.3526 Evaluate side-chains 971 residues out of total 4459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 963 time to evaluate : 4.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 105 ASN Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain C residue 565 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 416 optimal weight: 1.9990 chunk 373 optimal weight: 0.2980 chunk 207 optimal weight: 0.4980 chunk 127 optimal weight: 8.9990 chunk 252 optimal weight: 20.0000 chunk 199 optimal weight: 0.5980 chunk 386 optimal weight: 1.9990 chunk 149 optimal weight: 0.0980 chunk 234 optimal weight: 0.5980 chunk 287 optimal weight: 1.9990 chunk 447 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1517 GLN ** A1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1718 HIS A1769 GLN ** A2528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2594 HIS ** A3141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3435 GLN A3442 ASN A3625 GLN ** A3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3760 HIS ** A3765 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 HIS B 116 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN G 190 GLN G 197 HIS G 445 HIS ** G 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN E 228 GLN E 578 HIS E 590 ASN E 605 GLN E 655 HIS F 93 HIS C 468 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 38654 Z= 0.205 Angle : 0.649 14.746 52497 Z= 0.325 Chirality : 0.041 0.187 6036 Planarity : 0.005 0.068 6755 Dihedral : 6.318 86.185 5386 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.59 % Favored : 96.39 % Rotamer: Outliers : 2.63 % Allowed : 14.82 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.12), residues: 4851 helix: 1.89 (0.09), residues: 3045 sheet: -0.75 (0.36), residues: 195 loop : -0.69 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1821 HIS 0.010 0.001 HIS B 89 PHE 0.056 0.002 PHE A 995 TYR 0.023 0.002 TYR B 167 ARG 0.009 0.001 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 4459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1008 time to evaluate : 4.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ILE cc_start: 0.9307 (tp) cc_final: 0.8964 (pt) REVERT: A 402 SER cc_start: 0.9273 (t) cc_final: 0.9040 (p) REVERT: A 603 PHE cc_start: 0.8343 (m-10) cc_final: 0.8107 (m-10) REVERT: A 612 LYS cc_start: 0.8820 (tttt) cc_final: 0.8489 (tttt) REVERT: A 613 SER cc_start: 0.8132 (OUTLIER) cc_final: 0.7875 (p) REVERT: A 622 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8668 (mm) REVERT: A 665 THR cc_start: 0.8482 (m) cc_final: 0.8202 (t) REVERT: A 677 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7340 (tt0) REVERT: A 680 ARG cc_start: 0.8310 (tmm-80) cc_final: 0.7969 (ttp80) REVERT: A 681 GLU cc_start: 0.7913 (mt-10) cc_final: 0.6602 (mt-10) REVERT: A 690 MET cc_start: 0.7502 (mpp) cc_final: 0.6309 (mpp) REVERT: A 747 PHE cc_start: 0.6986 (m-10) cc_final: 0.6432 (m-80) REVERT: A 748 MET cc_start: 0.6755 (mpp) cc_final: 0.6432 (mpp) REVERT: A 795 SER cc_start: 0.7624 (m) cc_final: 0.7301 (t) REVERT: A 858 LYS cc_start: 0.7715 (mmmt) cc_final: 0.7273 (mmmm) REVERT: A 895 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6880 (mm-30) REVERT: A 912 LEU cc_start: 0.5761 (tp) cc_final: 0.5379 (tt) REVERT: A 944 LYS cc_start: 0.7203 (mmtm) cc_final: 0.6979 (mmtm) REVERT: A 1023 MET cc_start: 0.8583 (ptp) cc_final: 0.8164 (mtp) REVERT: A 1170 LEU cc_start: 0.8792 (mm) cc_final: 0.8569 (mp) REVERT: A 1222 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7418 (t80) REVERT: A 1417 ARG cc_start: 0.7474 (ptm-80) cc_final: 0.7159 (ptp90) REVERT: A 1509 TRP cc_start: 0.7938 (m100) cc_final: 0.7635 (m100) REVERT: A 1549 PHE cc_start: 0.7951 (p90) cc_final: 0.7707 (p90) REVERT: A 1554 MET cc_start: 0.7843 (tpp) cc_final: 0.7317 (tpt) REVERT: A 1586 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8453 (mp0) REVERT: A 1594 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8630 (tm-30) REVERT: A 1649 ASP cc_start: 0.8706 (t0) cc_final: 0.8258 (t0) REVERT: A 1709 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7358 (mp0) REVERT: A 1716 LEU cc_start: 0.8393 (mp) cc_final: 0.8090 (tp) REVERT: A 1718 HIS cc_start: 0.7155 (p90) cc_final: 0.6593 (p90) REVERT: A 1722 PHE cc_start: 0.8537 (m-80) cc_final: 0.7924 (m-80) REVERT: A 1740 ASP cc_start: 0.8646 (m-30) cc_final: 0.8360 (m-30) REVERT: A 1819 ASP cc_start: 0.8045 (m-30) cc_final: 0.7662 (p0) REVERT: A 1840 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7830 (mmt180) REVERT: A 1843 LEU cc_start: 0.7952 (mt) cc_final: 0.7407 (mt) REVERT: A 1872 TYR cc_start: 0.7576 (m-80) cc_final: 0.7149 (m-80) REVERT: A 1927 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7995 (tp) REVERT: A 2418 MET cc_start: 0.6564 (mmm) cc_final: 0.5768 (ptm) REVERT: A 2428 LEU cc_start: 0.6685 (mt) cc_final: 0.6415 (mt) REVERT: A 2459 ASP cc_start: 0.7519 (m-30) cc_final: 0.7261 (m-30) REVERT: A 2545 ASN cc_start: 0.7713 (m110) cc_final: 0.7010 (m110) REVERT: A 2587 LYS cc_start: 0.6700 (mttt) cc_final: 0.6462 (mmmt) REVERT: A 2589 LEU cc_start: 0.6997 (mt) cc_final: 0.6601 (mt) REVERT: A 2595 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7964 (tp) REVERT: A 2673 GLU cc_start: 0.6923 (mm-30) cc_final: 0.6720 (mm-30) REVERT: A 2676 MET cc_start: 0.7230 (mmm) cc_final: 0.6840 (mmm) REVERT: A 2763 GLU cc_start: 0.7514 (pp20) cc_final: 0.7269 (pt0) REVERT: A 2862 SER cc_start: 0.7364 (t) cc_final: 0.6996 (p) REVERT: A 2898 ASN cc_start: 0.6922 (m-40) cc_final: 0.6604 (m-40) REVERT: A 2958 LYS cc_start: 0.7314 (mmtt) cc_final: 0.6889 (mmtt) REVERT: A 3500 LEU cc_start: 0.7714 (tp) cc_final: 0.7459 (tt) REVERT: A 3537 ASN cc_start: 0.7365 (p0) cc_final: 0.7157 (p0) REVERT: A 3562 GLU cc_start: 0.7542 (tp30) cc_final: 0.7238 (tp30) REVERT: A 3614 SER cc_start: 0.7341 (t) cc_final: 0.7101 (p) REVERT: A 3624 LYS cc_start: 0.7257 (tttp) cc_final: 0.6881 (mtpp) REVERT: A 3711 LYS cc_start: 0.8339 (mmmt) cc_final: 0.8079 (mmmm) REVERT: A 3726 ILE cc_start: 0.7196 (mt) cc_final: 0.6762 (mt) REVERT: B 72 ILE cc_start: 0.8892 (tp) cc_final: 0.8683 (tt) REVERT: B 108 GLU cc_start: 0.7563 (pp20) cc_final: 0.6942 (pp20) REVERT: B 170 PHE cc_start: 0.5562 (t80) cc_final: 0.5236 (t80) REVERT: B 187 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8839 (p) REVERT: B 192 LYS cc_start: 0.7998 (ptpp) cc_final: 0.7676 (ptpp) REVERT: B 229 GLN cc_start: 0.7866 (pp30) cc_final: 0.7533 (pt0) REVERT: B 281 ASN cc_start: 0.8296 (m-40) cc_final: 0.7902 (m-40) REVERT: B 293 GLU cc_start: 0.7744 (mp0) cc_final: 0.7387 (mp0) REVERT: B 297 ASN cc_start: 0.8629 (m-40) cc_final: 0.8093 (m-40) REVERT: B 318 LEU cc_start: 0.8467 (tt) cc_final: 0.8097 (mm) REVERT: G 285 PHE cc_start: 0.8043 (m-80) cc_final: 0.7690 (m-80) REVERT: G 297 LEU cc_start: 0.7531 (mt) cc_final: 0.7265 (mt) REVERT: G 407 LEU cc_start: 0.8447 (mt) cc_final: 0.8235 (mt) REVERT: G 462 LEU cc_start: 0.8459 (tp) cc_final: 0.8227 (tp) REVERT: E 203 ILE cc_start: 0.8242 (mm) cc_final: 0.8031 (mm) REVERT: E 249 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6640 (mm-30) REVERT: E 310 GLU cc_start: 0.7179 (tp30) cc_final: 0.6809 (tp30) REVERT: E 582 ARG cc_start: 0.6512 (mmp80) cc_final: 0.6027 (mmp80) REVERT: F 111 GLU cc_start: 0.7832 (tt0) cc_final: 0.7422 (tt0) REVERT: F 266 GLU cc_start: 0.7995 (pm20) cc_final: 0.7790 (pm20) REVERT: F 272 MET cc_start: 0.6874 (tmm) cc_final: 0.6633 (tmm) REVERT: F 342 GLU cc_start: 0.6674 (mm-30) cc_final: 0.6444 (mm-30) REVERT: C 419 MET cc_start: 0.1130 (ttt) cc_final: 0.0892 (ttt) REVERT: C 429 THR cc_start: 0.5969 (t) cc_final: 0.5653 (m) REVERT: C 439 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7999 (mm-30) REVERT: C 506 GLU cc_start: 0.7793 (mp0) cc_final: 0.7100 (mp0) REVERT: C 511 ILE cc_start: 0.8306 (mm) cc_final: 0.8084 (mm) REVERT: C 512 LYS cc_start: 0.8216 (tppt) cc_final: 0.7941 (mppt) REVERT: C 513 ASP cc_start: 0.6574 (t0) cc_final: 0.6310 (t70) outliers start: 100 outliers final: 54 residues processed: 1052 average time/residue: 0.5159 time to fit residues: 893.4709 Evaluate side-chains 954 residues out of total 4459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 894 time to evaluate : 4.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1222 PHE Chi-restraints excluded: chain A residue 1424 PHE Chi-restraints excluded: chain A residue 1690 SER Chi-restraints excluded: chain A residue 1701 GLU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1743 ILE Chi-restraints excluded: chain A residue 1846 LEU Chi-restraints excluded: chain A residue 1927 LEU Chi-restraints excluded: chain A residue 2535 VAL Chi-restraints excluded: chain A residue 2595 ILE Chi-restraints excluded: chain A residue 2625 VAL Chi-restraints excluded: chain A residue 2729 SER Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 2811 THR Chi-restraints excluded: chain A residue 3157 ILE Chi-restraints excluded: chain A residue 3175 THR Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3539 ASP Chi-restraints excluded: chain A residue 3579 LEU Chi-restraints excluded: chain A residue 3740 MET Chi-restraints excluded: chain A residue 3795 ASN Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 259 GLU Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 504 ILE Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain F residue 298 ASP Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 565 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 248 optimal weight: 0.9990 chunk 138 optimal weight: 0.6980 chunk 372 optimal weight: 0.7980 chunk 304 optimal weight: 0.7980 chunk 123 optimal weight: 20.0000 chunk 448 optimal weight: 0.7980 chunk 484 optimal weight: 9.9990 chunk 399 optimal weight: 1.9990 chunk 444 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 359 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1517 GLN ** A1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1555 ASN A1769 GLN A2461 ASN ** A2528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2901 ASN ** A3418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3435 GLN A3442 ASN A3558 GLN ** A3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN E 240 HIS E 655 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 38654 Z= 0.242 Angle : 0.628 12.302 52497 Z= 0.314 Chirality : 0.041 0.231 6036 Planarity : 0.005 0.060 6755 Dihedral : 6.158 88.647 5380 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.69 % Favored : 96.29 % Rotamer: Outliers : 3.11 % Allowed : 18.30 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.12), residues: 4851 helix: 1.79 (0.09), residues: 3045 sheet: -0.77 (0.36), residues: 186 loop : -0.72 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 87 HIS 0.029 0.001 HIS B 29 PHE 0.037 0.002 PHE A 995 TYR 0.020 0.002 TYR B 134 ARG 0.007 0.001 ARG A2576 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 4459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 969 time to evaluate : 4.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ILE cc_start: 0.9285 (tp) cc_final: 0.9005 (pt) REVERT: A 325 HIS cc_start: 0.7741 (m-70) cc_final: 0.6982 (m-70) REVERT: A 330 ILE cc_start: 0.9015 (mm) cc_final: 0.8380 (tp) REVERT: A 410 MET cc_start: 0.8020 (ppp) cc_final: 0.7813 (ppp) REVERT: A 433 GLN cc_start: 0.8306 (mm110) cc_final: 0.8022 (mm-40) REVERT: A 612 LYS cc_start: 0.8808 (tttt) cc_final: 0.8372 (ttpt) REVERT: A 655 GLU cc_start: 0.7763 (pp20) cc_final: 0.7469 (pp20) REVERT: A 665 THR cc_start: 0.8479 (m) cc_final: 0.8202 (t) REVERT: A 666 MET cc_start: 0.7545 (ptt) cc_final: 0.7030 (ptt) REVERT: A 677 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7527 (tt0) REVERT: A 680 ARG cc_start: 0.8364 (tmm-80) cc_final: 0.8029 (ttp-110) REVERT: A 681 GLU cc_start: 0.7958 (mt-10) cc_final: 0.6899 (mt-10) REVERT: A 686 MET cc_start: 0.6983 (tpp) cc_final: 0.6546 (tpp) REVERT: A 689 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8196 (mm-40) REVERT: A 690 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6018 (mpp) REVERT: A 692 ASP cc_start: 0.7087 (t70) cc_final: 0.6428 (t70) REVERT: A 747 PHE cc_start: 0.7015 (m-10) cc_final: 0.6462 (m-80) REVERT: A 795 SER cc_start: 0.7671 (m) cc_final: 0.7443 (t) REVERT: A 888 GLU cc_start: 0.7115 (pm20) cc_final: 0.6844 (pm20) REVERT: A 907 LYS cc_start: 0.7553 (ttmm) cc_final: 0.7337 (ttmm) REVERT: A 912 LEU cc_start: 0.6080 (tp) cc_final: 0.5731 (tt) REVERT: A 970 ILE cc_start: 0.8471 (tp) cc_final: 0.8171 (tp) REVERT: A 1023 MET cc_start: 0.8564 (ptp) cc_final: 0.8125 (mtp) REVERT: A 1222 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7595 (t80) REVERT: A 1420 ILE cc_start: 0.8794 (tt) cc_final: 0.8561 (tp) REVERT: A 1509 TRP cc_start: 0.7907 (m100) cc_final: 0.7637 (m100) REVERT: A 1554 MET cc_start: 0.7845 (tpp) cc_final: 0.7337 (tpt) REVERT: A 1579 PHE cc_start: 0.8764 (t80) cc_final: 0.8530 (t80) REVERT: A 1586 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8574 (mp0) REVERT: A 1594 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8670 (tm-30) REVERT: A 1649 ASP cc_start: 0.8856 (t0) cc_final: 0.8441 (t0) REVERT: A 1740 ASP cc_start: 0.8643 (m-30) cc_final: 0.8367 (m-30) REVERT: A 1843 LEU cc_start: 0.7772 (mt) cc_final: 0.7444 (mt) REVERT: A 1970 PHE cc_start: 0.6505 (t80) cc_final: 0.5946 (t80) REVERT: A 2418 MET cc_start: 0.6788 (mmm) cc_final: 0.5946 (ptm) REVERT: A 2428 LEU cc_start: 0.6877 (mt) cc_final: 0.6601 (mt) REVERT: A 2587 LYS cc_start: 0.7493 (mttt) cc_final: 0.7097 (mmmt) REVERT: A 2589 LEU cc_start: 0.7417 (mt) cc_final: 0.7126 (mt) REVERT: A 2645 LEU cc_start: 0.7180 (mp) cc_final: 0.6953 (mp) REVERT: A 2898 ASN cc_start: 0.7303 (m-40) cc_final: 0.6905 (m-40) REVERT: A 2958 LYS cc_start: 0.7651 (mmtt) cc_final: 0.7097 (mmtt) REVERT: A 3538 ASP cc_start: 0.7974 (t0) cc_final: 0.7650 (t0) REVERT: A 3562 GLU cc_start: 0.7757 (tp30) cc_final: 0.7487 (tp30) REVERT: A 3614 SER cc_start: 0.7722 (t) cc_final: 0.7489 (p) REVERT: A 3709 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7662 (mp) REVERT: A 3711 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8281 (mmmm) REVERT: A 3726 ILE cc_start: 0.7576 (mt) cc_final: 0.7198 (mt) REVERT: B 72 ILE cc_start: 0.8904 (tp) cc_final: 0.8575 (tt) REVERT: B 108 GLU cc_start: 0.7605 (pp20) cc_final: 0.7036 (pp20) REVERT: B 133 PHE cc_start: 0.7966 (t80) cc_final: 0.7096 (t80) REVERT: B 187 THR cc_start: 0.9109 (m) cc_final: 0.8887 (p) REVERT: B 192 LYS cc_start: 0.7994 (ptpp) cc_final: 0.7716 (ptpp) REVERT: B 254 GLU cc_start: 0.8059 (mp0) cc_final: 0.7630 (mp0) REVERT: B 293 GLU cc_start: 0.7835 (mp0) cc_final: 0.7626 (mp0) REVERT: B 297 ASN cc_start: 0.8689 (m-40) cc_final: 0.8227 (m-40) REVERT: B 318 LEU cc_start: 0.8459 (tt) cc_final: 0.8068 (mm) REVERT: G 61 MET cc_start: 0.7937 (mtm) cc_final: 0.7696 (mtp) REVERT: G 297 LEU cc_start: 0.7678 (mt) cc_final: 0.7358 (mt) REVERT: G 407 LEU cc_start: 0.8507 (mt) cc_final: 0.8296 (mt) REVERT: G 462 LEU cc_start: 0.8537 (tp) cc_final: 0.8316 (tp) REVERT: E 200 LYS cc_start: 0.8378 (mttt) cc_final: 0.8111 (mtpt) REVERT: E 203 ILE cc_start: 0.8367 (mm) cc_final: 0.8072 (mm) REVERT: E 249 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6674 (mm-30) REVERT: E 582 ARG cc_start: 0.6662 (mmp80) cc_final: 0.6204 (mmp80) REVERT: F 111 GLU cc_start: 0.7783 (tt0) cc_final: 0.7334 (tt0) REVERT: F 266 GLU cc_start: 0.8039 (pm20) cc_final: 0.7834 (pm20) REVERT: F 284 GLU cc_start: 0.6770 (tp30) cc_final: 0.6548 (tp30) REVERT: F 285 ARG cc_start: 0.8478 (ptm160) cc_final: 0.8250 (ptp-170) REVERT: F 340 VAL cc_start: 0.8958 (t) cc_final: 0.8681 (m) REVERT: F 342 GLU cc_start: 0.6745 (mm-30) cc_final: 0.6410 (mm-30) REVERT: C 419 MET cc_start: 0.1324 (ttt) cc_final: 0.1042 (ttt) REVERT: C 429 THR cc_start: 0.5897 (t) cc_final: 0.5655 (m) REVERT: C 511 ILE cc_start: 0.8453 (mm) cc_final: 0.8196 (mm) REVERT: C 575 LEU cc_start: 0.7174 (tp) cc_final: 0.6646 (tt) outliers start: 118 outliers final: 69 residues processed: 1023 average time/residue: 0.5099 time to fit residues: 859.0302 Evaluate side-chains 931 residues out of total 4459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 859 time to evaluate : 5.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 809 MET Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1222 PHE Chi-restraints excluded: chain A residue 1424 PHE Chi-restraints excluded: chain A residue 1592 PHE Chi-restraints excluded: chain A residue 1701 GLU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1743 ILE Chi-restraints excluded: chain A residue 2535 VAL Chi-restraints excluded: chain A residue 2625 VAL Chi-restraints excluded: chain A residue 2667 VAL Chi-restraints excluded: chain A residue 2729 SER Chi-restraints excluded: chain A residue 2751 LEU Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 2811 THR Chi-restraints excluded: chain A residue 3078 PHE Chi-restraints excluded: chain A residue 3146 LEU Chi-restraints excluded: chain A residue 3157 ILE Chi-restraints excluded: chain A residue 3175 THR Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3509 SER Chi-restraints excluded: chain A residue 3579 LEU Chi-restraints excluded: chain A residue 3709 ILE Chi-restraints excluded: chain A residue 3739 ASP Chi-restraints excluded: chain A residue 3740 MET Chi-restraints excluded: chain A residue 3795 ASN Chi-restraints excluded: chain A residue 3819 SER Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 8 TYR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 259 GLU Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 497 ASP Chi-restraints excluded: chain E residue 504 ILE Chi-restraints excluded: chain E residue 523 PHE Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 608 ASP Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 619 SER Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 443 optimal weight: 1.9990 chunk 337 optimal weight: 3.9990 chunk 232 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 214 optimal weight: 0.9990 chunk 301 optimal weight: 0.3980 chunk 450 optimal weight: 0.5980 chunk 476 optimal weight: 0.5980 chunk 235 optimal weight: 0.8980 chunk 426 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN A 397 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1555 ASN A1704 GLN ** A1718 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2460 GLN A2461 ASN ** A2528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2653 ASN ** A3141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3442 ASN A3537 ASN A3558 GLN ** A3643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 HIS B 253 ASN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 655 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38654 Z= 0.202 Angle : 0.619 13.723 52497 Z= 0.307 Chirality : 0.040 0.264 6036 Planarity : 0.005 0.065 6755 Dihedral : 6.056 88.569 5377 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.83 % Favored : 96.15 % Rotamer: Outliers : 3.87 % Allowed : 19.93 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.12), residues: 4851 helix: 1.74 (0.09), residues: 3050 sheet: -0.88 (0.36), residues: 184 loop : -0.69 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 87 HIS 0.010 0.001 HIS A1540 PHE 0.041 0.002 PHE A1549 TYR 0.022 0.001 TYR F 321 ARG 0.011 0.001 ARG A2576 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1073 residues out of total 4459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 926 time to evaluate : 4.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ILE cc_start: 0.9286 (tp) cc_final: 0.9016 (pt) REVERT: A 330 ILE cc_start: 0.9042 (mm) cc_final: 0.8467 (tp) REVERT: A 360 TYR cc_start: 0.8244 (t80) cc_final: 0.7778 (t80) REVERT: A 612 LYS cc_start: 0.8810 (tttt) cc_final: 0.8551 (tttt) REVERT: A 666 MET cc_start: 0.7504 (ptt) cc_final: 0.6936 (ptt) REVERT: A 667 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7398 (t80) REVERT: A 677 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7496 (tt0) REVERT: A 680 ARG cc_start: 0.8359 (tmm-80) cc_final: 0.8042 (ttp-110) REVERT: A 681 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7492 (mt-10) REVERT: A 686 MET cc_start: 0.6992 (tpp) cc_final: 0.6430 (tpp) REVERT: A 690 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.5797 (mpp) REVERT: A 747 PHE cc_start: 0.6969 (m-10) cc_final: 0.6361 (m-80) REVERT: A 795 SER cc_start: 0.7746 (m) cc_final: 0.7309 (t) REVERT: A 858 LYS cc_start: 0.8273 (tppt) cc_final: 0.7684 (mmmm) REVERT: A 865 ASN cc_start: 0.7722 (m-40) cc_final: 0.7492 (m-40) REVERT: A 912 LEU cc_start: 0.6157 (tp) cc_final: 0.5761 (tt) REVERT: A 1023 MET cc_start: 0.8520 (ptp) cc_final: 0.7993 (mtp) REVERT: A 1222 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7491 (t80) REVERT: A 1420 ILE cc_start: 0.8853 (tt) cc_final: 0.8596 (tp) REVERT: A 1509 TRP cc_start: 0.7937 (m100) cc_final: 0.7722 (m100) REVERT: A 1537 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8411 (p0) REVERT: A 1554 MET cc_start: 0.7721 (tpp) cc_final: 0.7243 (tpt) REVERT: A 1558 LEU cc_start: 0.8850 (tp) cc_final: 0.8567 (tp) REVERT: A 1579 PHE cc_start: 0.8789 (t80) cc_final: 0.8546 (t80) REVERT: A 1586 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8625 (mp0) REVERT: A 1594 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8733 (tm-30) REVERT: A 1649 ASP cc_start: 0.8877 (t0) cc_final: 0.8379 (t0) REVERT: A 1843 LEU cc_start: 0.7842 (mt) cc_final: 0.7589 (mt) REVERT: A 1872 TYR cc_start: 0.7400 (m-80) cc_final: 0.7196 (m-10) REVERT: A 1874 LYS cc_start: 0.8114 (mttm) cc_final: 0.7574 (mttm) REVERT: A 1970 PHE cc_start: 0.6468 (t80) cc_final: 0.5891 (t80) REVERT: A 2418 MET cc_start: 0.6836 (mmm) cc_final: 0.6030 (ptm) REVERT: A 2428 LEU cc_start: 0.6965 (mt) cc_final: 0.6682 (mt) REVERT: A 2547 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7801 (tp) REVERT: A 2587 LYS cc_start: 0.7657 (mttt) cc_final: 0.7200 (mmmt) REVERT: A 2589 LEU cc_start: 0.7707 (mt) cc_final: 0.7365 (mt) REVERT: A 2643 GLU cc_start: 0.5989 (mt-10) cc_final: 0.5770 (mt-10) REVERT: A 2645 LEU cc_start: 0.7374 (mp) cc_final: 0.7142 (mp) REVERT: A 2714 ILE cc_start: 0.8162 (mm) cc_final: 0.7946 (mt) REVERT: A 2895 ASP cc_start: 0.7688 (m-30) cc_final: 0.7485 (m-30) REVERT: A 2958 LYS cc_start: 0.7741 (mmtt) cc_final: 0.7149 (mmtt) REVERT: A 3129 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: A 3443 ASN cc_start: 0.6303 (t0) cc_final: 0.5951 (t160) REVERT: A 3538 ASP cc_start: 0.7882 (t0) cc_final: 0.7501 (t0) REVERT: A 3562 GLU cc_start: 0.7805 (tp30) cc_final: 0.7572 (tp30) REVERT: A 3624 LYS cc_start: 0.7667 (tttp) cc_final: 0.7348 (ttpp) REVERT: A 3673 LYS cc_start: 0.7858 (mmtm) cc_final: 0.7069 (mptt) REVERT: A 3709 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7793 (mp) REVERT: A 3711 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8432 (mmmm) REVERT: A 3726 ILE cc_start: 0.7720 (mt) cc_final: 0.7268 (mt) REVERT: A 3729 ILE cc_start: 0.7777 (mt) cc_final: 0.7429 (mp) REVERT: A 3737 GLU cc_start: 0.3951 (OUTLIER) cc_final: 0.3522 (mp0) REVERT: B 72 ILE cc_start: 0.8771 (tp) cc_final: 0.8539 (tt) REVERT: B 108 GLU cc_start: 0.7639 (pp20) cc_final: 0.7015 (pp20) REVERT: B 187 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8907 (p) REVERT: B 192 LYS cc_start: 0.8032 (ptpp) cc_final: 0.7744 (ptpp) REVERT: B 229 GLN cc_start: 0.7847 (pp30) cc_final: 0.7483 (pt0) REVERT: B 297 ASN cc_start: 0.8715 (m-40) cc_final: 0.8295 (m-40) REVERT: B 318 LEU cc_start: 0.8499 (tt) cc_final: 0.8128 (mm) REVERT: B 350 LEU cc_start: 0.8612 (mt) cc_final: 0.8195 (mm) REVERT: G 61 MET cc_start: 0.7847 (mtm) cc_final: 0.7610 (mtp) REVERT: G 297 LEU cc_start: 0.7698 (mt) cc_final: 0.7378 (mt) REVERT: E 203 ILE cc_start: 0.8426 (mm) cc_final: 0.8162 (mm) REVERT: E 426 MET cc_start: 0.7243 (tpp) cc_final: 0.6940 (tpp) REVERT: E 465 PHE cc_start: 0.8078 (t80) cc_final: 0.7868 (t80) REVERT: E 582 ARG cc_start: 0.6795 (mmp80) cc_final: 0.6067 (mmp80) REVERT: F 285 ARG cc_start: 0.8470 (ptm160) cc_final: 0.8203 (ptp-170) REVERT: F 340 VAL cc_start: 0.8965 (t) cc_final: 0.8661 (m) REVERT: C 429 THR cc_start: 0.5899 (t) cc_final: 0.5644 (m) REVERT: C 435 ASN cc_start: 0.7123 (m-40) cc_final: 0.6722 (t0) REVERT: C 439 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7796 (mm-30) REVERT: C 450 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7787 (ttp-110) REVERT: C 459 TRP cc_start: 0.8227 (m100) cc_final: 0.8013 (m100) REVERT: C 511 ILE cc_start: 0.8417 (mm) cc_final: 0.8173 (mm) outliers start: 147 outliers final: 86 residues processed: 991 average time/residue: 0.5165 time to fit residues: 849.8982 Evaluate side-chains 954 residues out of total 4459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 858 time to evaluate : 4.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 560 ASP Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 667 PHE Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1222 PHE Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1421 LEU Chi-restraints excluded: chain A residue 1537 ASP Chi-restraints excluded: chain A residue 1592 PHE Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1701 GLU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1720 LYS Chi-restraints excluded: chain A residue 1743 ILE Chi-restraints excluded: chain A residue 1841 LEU Chi-restraints excluded: chain A residue 2535 VAL Chi-restraints excluded: chain A residue 2547 LEU Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2625 VAL Chi-restraints excluded: chain A residue 2667 VAL Chi-restraints excluded: chain A residue 2729 SER Chi-restraints excluded: chain A residue 2730 LEU Chi-restraints excluded: chain A residue 2742 LEU Chi-restraints excluded: chain A residue 2751 LEU Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 2914 ILE Chi-restraints excluded: chain A residue 2961 MET Chi-restraints excluded: chain A residue 3078 PHE Chi-restraints excluded: chain A residue 3129 GLU Chi-restraints excluded: chain A residue 3146 LEU Chi-restraints excluded: chain A residue 3157 ILE Chi-restraints excluded: chain A residue 3175 THR Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3579 LEU Chi-restraints excluded: chain A residue 3584 ILE Chi-restraints excluded: chain A residue 3709 ILE Chi-restraints excluded: chain A residue 3718 LEU Chi-restraints excluded: chain A residue 3734 SER Chi-restraints excluded: chain A residue 3737 GLU Chi-restraints excluded: chain A residue 3739 ASP Chi-restraints excluded: chain A residue 3740 MET Chi-restraints excluded: chain A residue 3795 ASN Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 8 TYR Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 259 GLU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 497 ASP Chi-restraints excluded: chain E residue 504 ILE Chi-restraints excluded: chain E residue 523 PHE Chi-restraints excluded: chain E residue 612 PHE Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 450 ARG Chi-restraints excluded: chain C residue 472 GLN Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 608 ASP Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 396 optimal weight: 0.6980 chunk 270 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 354 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 406 optimal weight: 0.4980 chunk 329 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 243 optimal weight: 0.5980 chunk 427 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 HIS ** A1386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3442 ASN A3537 ASN A3651 HIS B 29 HIS ** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 386 ASN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 655 HIS C 461 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 38654 Z= 0.190 Angle : 0.606 12.671 52497 Z= 0.298 Chirality : 0.040 0.222 6036 Planarity : 0.005 0.059 6755 Dihedral : 5.925 85.412 5377 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.71 % Favored : 96.27 % Rotamer: Outliers : 3.55 % Allowed : 21.09 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.12), residues: 4851 helix: 1.75 (0.09), residues: 3051 sheet: -0.74 (0.37), residues: 179 loop : -0.71 (0.16), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A2906 HIS 0.026 0.001 HIS B 29 PHE 0.039 0.002 PHE A1722 TYR 0.021 0.001 TYR A2737 ARG 0.012 0.000 ARG A2576 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 4459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 904 time to evaluate : 4.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ILE cc_start: 0.9252 (tp) cc_final: 0.8941 (pt) REVERT: A 447 LYS cc_start: 0.8633 (mtmt) cc_final: 0.8230 (mtmt) REVERT: A 610 ILE cc_start: 0.9053 (tp) cc_final: 0.8674 (mt) REVERT: A 612 LYS cc_start: 0.8804 (tttt) cc_final: 0.8435 (tttt) REVERT: A 677 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7606 (tt0) REVERT: A 681 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7007 (mt-10) REVERT: A 686 MET cc_start: 0.6943 (tpp) cc_final: 0.6477 (tpp) REVERT: A 690 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.5600 (mpp) REVERT: A 802 GLU cc_start: 0.5787 (OUTLIER) cc_final: 0.5509 (mp0) REVERT: A 815 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7736 (tt) REVERT: A 865 ASN cc_start: 0.7792 (m-40) cc_final: 0.7346 (m-40) REVERT: A 903 GLU cc_start: 0.6869 (tm-30) cc_final: 0.6270 (tm-30) REVERT: A 912 LEU cc_start: 0.6238 (tp) cc_final: 0.5924 (tt) REVERT: A 970 ILE cc_start: 0.8473 (tp) cc_final: 0.8226 (tp) REVERT: A 1023 MET cc_start: 0.8501 (ptp) cc_final: 0.8013 (mtp) REVERT: A 1335 ASP cc_start: 0.7807 (t0) cc_final: 0.7409 (t0) REVERT: A 1420 ILE cc_start: 0.8912 (tt) cc_final: 0.8683 (tp) REVERT: A 1522 ASP cc_start: 0.8478 (m-30) cc_final: 0.7924 (t70) REVERT: A 1554 MET cc_start: 0.7685 (tpp) cc_final: 0.7282 (tpt) REVERT: A 1558 LEU cc_start: 0.8826 (tp) cc_final: 0.8530 (tp) REVERT: A 1579 PHE cc_start: 0.8792 (t80) cc_final: 0.8541 (t80) REVERT: A 1586 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8614 (mp0) REVERT: A 1649 ASP cc_start: 0.8911 (t0) cc_final: 0.8368 (t0) REVERT: A 1740 ASP cc_start: 0.8632 (m-30) cc_final: 0.8317 (m-30) REVERT: A 1843 LEU cc_start: 0.7869 (mt) cc_final: 0.7526 (mt) REVERT: A 1872 TYR cc_start: 0.7389 (m-80) cc_final: 0.7151 (m-10) REVERT: A 1874 LYS cc_start: 0.8201 (mttm) cc_final: 0.7667 (mttm) REVERT: A 2418 MET cc_start: 0.6881 (mmm) cc_final: 0.6072 (ptm) REVERT: A 2423 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7569 (mt) REVERT: A 2428 LEU cc_start: 0.7138 (mt) cc_final: 0.6851 (mt) REVERT: A 2479 TYR cc_start: 0.7901 (m-10) cc_final: 0.7472 (m-10) REVERT: A 2547 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7950 (tp) REVERT: A 2587 LYS cc_start: 0.7795 (mttt) cc_final: 0.7290 (mtpt) REVERT: A 2589 LEU cc_start: 0.7889 (mt) cc_final: 0.7535 (mt) REVERT: A 2595 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.7978 (tp) REVERT: A 2628 LEU cc_start: 0.7558 (mt) cc_final: 0.7263 (mt) REVERT: A 2643 GLU cc_start: 0.6093 (mt-10) cc_final: 0.5818 (mt-10) REVERT: A 2714 ILE cc_start: 0.8288 (mm) cc_final: 0.8056 (mt) REVERT: A 2895 ASP cc_start: 0.7870 (m-30) cc_final: 0.7638 (m-30) REVERT: A 2958 LYS cc_start: 0.7650 (mmtt) cc_final: 0.7223 (mmtt) REVERT: A 3098 LYS cc_start: 0.7876 (pptt) cc_final: 0.7407 (pttt) REVERT: A 3443 ASN cc_start: 0.6459 (t0) cc_final: 0.6133 (t160) REVERT: A 3538 ASP cc_start: 0.7912 (t0) cc_final: 0.7516 (t0) REVERT: A 3570 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8137 (ttmm) REVERT: A 3607 ASP cc_start: 0.6808 (m-30) cc_final: 0.6556 (m-30) REVERT: A 3640 MET cc_start: 0.7839 (mmm) cc_final: 0.7566 (mmm) REVERT: A 3673 LYS cc_start: 0.7835 (mmtm) cc_final: 0.7428 (mptt) REVERT: A 3711 LYS cc_start: 0.8769 (mmmt) cc_final: 0.8496 (mmmm) REVERT: A 3726 ILE cc_start: 0.7687 (mt) cc_final: 0.7384 (mt) REVERT: A 3729 ILE cc_start: 0.7777 (mt) cc_final: 0.7549 (mt) REVERT: B 108 GLU cc_start: 0.7663 (pp20) cc_final: 0.7097 (pp20) REVERT: B 192 LYS cc_start: 0.8040 (ptpp) cc_final: 0.7738 (ptpp) REVERT: B 254 GLU cc_start: 0.8139 (mp0) cc_final: 0.7741 (mp0) REVERT: B 297 ASN cc_start: 0.8707 (m-40) cc_final: 0.8360 (m-40) REVERT: B 318 LEU cc_start: 0.8515 (tt) cc_final: 0.8245 (mm) REVERT: G 61 MET cc_start: 0.7781 (mtm) cc_final: 0.7479 (mtp) REVERT: G 297 LEU cc_start: 0.7781 (mt) cc_final: 0.7518 (mt) REVERT: E 203 ILE cc_start: 0.8450 (mm) cc_final: 0.8148 (mm) REVERT: E 249 GLU cc_start: 0.7021 (mm-30) cc_final: 0.6567 (mm-30) REVERT: E 253 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7387 (mt) REVERT: E 426 MET cc_start: 0.7296 (tpp) cc_final: 0.7008 (tpp) REVERT: F 263 ASP cc_start: 0.8291 (t0) cc_final: 0.8053 (t0) REVERT: F 265 TYR cc_start: 0.6822 (t80) cc_final: 0.5787 (t80) REVERT: F 268 ASP cc_start: 0.6919 (p0) cc_final: 0.6681 (p0) REVERT: F 285 ARG cc_start: 0.8458 (ptm160) cc_final: 0.8253 (ptp-170) REVERT: C 429 THR cc_start: 0.5836 (t) cc_final: 0.5614 (m) REVERT: C 435 ASN cc_start: 0.7213 (m-40) cc_final: 0.6777 (t0) REVERT: C 439 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7751 (mm-30) REVERT: C 511 ILE cc_start: 0.8468 (mm) cc_final: 0.8220 (mm) REVERT: C 617 LEU cc_start: 0.8441 (mt) cc_final: 0.7938 (mm) REVERT: C 652 CYS cc_start: 0.7511 (t) cc_final: 0.7104 (m) outliers start: 135 outliers final: 89 residues processed: 968 average time/residue: 0.5094 time to fit residues: 819.4292 Evaluate side-chains 947 residues out of total 4459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 850 time to evaluate : 4.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 1005 PHE Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1421 LEU Chi-restraints excluded: chain A residue 1644 PHE Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1701 GLU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1743 ILE Chi-restraints excluded: chain A residue 1841 LEU Chi-restraints excluded: chain A residue 2423 LEU Chi-restraints excluded: chain A residue 2535 VAL Chi-restraints excluded: chain A residue 2547 LEU Chi-restraints excluded: chain A residue 2595 ILE Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2614 LYS Chi-restraints excluded: chain A residue 2625 VAL Chi-restraints excluded: chain A residue 2729 SER Chi-restraints excluded: chain A residue 2730 LEU Chi-restraints excluded: chain A residue 2742 LEU Chi-restraints excluded: chain A residue 2762 LEU Chi-restraints excluded: chain A residue 2961 MET Chi-restraints excluded: chain A residue 2963 GLU Chi-restraints excluded: chain A residue 3078 PHE Chi-restraints excluded: chain A residue 3146 LEU Chi-restraints excluded: chain A residue 3157 ILE Chi-restraints excluded: chain A residue 3167 GLN Chi-restraints excluded: chain A residue 3175 THR Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3509 SER Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3570 LYS Chi-restraints excluded: chain A residue 3579 LEU Chi-restraints excluded: chain A residue 3584 ILE Chi-restraints excluded: chain A residue 3661 THR Chi-restraints excluded: chain A residue 3718 LEU Chi-restraints excluded: chain A residue 3739 ASP Chi-restraints excluded: chain A residue 3740 MET Chi-restraints excluded: chain A residue 3795 ASN Chi-restraints excluded: chain A residue 3819 SER Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 8 TYR Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 259 GLU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 390 THR Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 497 ASP Chi-restraints excluded: chain E residue 504 ILE Chi-restraints excluded: chain E residue 612 PHE Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain F residue 298 ASP Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 619 SER Chi-restraints excluded: chain C residue 622 SER Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 160 optimal weight: 0.9990 chunk 429 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 279 optimal weight: 30.0000 chunk 117 optimal weight: 5.9990 chunk 476 optimal weight: 0.0020 chunk 395 optimal weight: 0.8980 chunk 220 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 250 optimal weight: 50.0000 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3490 HIS A3537 ASN ** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 655 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 38654 Z= 0.210 Angle : 0.617 12.176 52497 Z= 0.305 Chirality : 0.041 0.305 6036 Planarity : 0.005 0.057 6755 Dihedral : 5.858 82.516 5377 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.88 % Favored : 96.10 % Rotamer: Outliers : 3.98 % Allowed : 22.06 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.12), residues: 4851 helix: 1.76 (0.10), residues: 3053 sheet: -0.77 (0.35), residues: 190 loop : -0.74 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 87 HIS 0.007 0.001 HIS A1540 PHE 0.034 0.002 PHE A1549 TYR 0.020 0.001 TYR A 563 ARG 0.007 0.000 ARG A3541 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 4459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 895 time to evaluate : 4.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ILE cc_start: 0.9240 (tp) cc_final: 0.8931 (pt) REVERT: A 330 ILE cc_start: 0.9077 (mm) cc_final: 0.8434 (tp) REVERT: A 433 GLN cc_start: 0.8488 (mm110) cc_final: 0.8223 (mm-40) REVERT: A 610 ILE cc_start: 0.9040 (tp) cc_final: 0.8672 (mt) REVERT: A 612 LYS cc_start: 0.8797 (tttt) cc_final: 0.8469 (tttt) REVERT: A 666 MET cc_start: 0.7334 (ptt) cc_final: 0.7113 (ptt) REVERT: A 677 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7518 (tt0) REVERT: A 680 ARG cc_start: 0.8419 (tmm-80) cc_final: 0.8172 (tmm-80) REVERT: A 681 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7132 (mt-10) REVERT: A 690 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6836 (mmp) REVERT: A 802 GLU cc_start: 0.5932 (OUTLIER) cc_final: 0.5682 (mp0) REVERT: A 815 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7665 (tt) REVERT: A 838 LEU cc_start: 0.8529 (mm) cc_final: 0.8276 (mm) REVERT: A 865 ASN cc_start: 0.7952 (m-40) cc_final: 0.7716 (m-40) REVERT: A 929 LEU cc_start: 0.8462 (mt) cc_final: 0.8187 (mt) REVERT: A 970 ILE cc_start: 0.8533 (tp) cc_final: 0.8267 (tp) REVERT: A 1145 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7384 (tt0) REVERT: A 1335 ASP cc_start: 0.7874 (t0) cc_final: 0.7426 (t0) REVERT: A 1522 ASP cc_start: 0.8531 (m-30) cc_final: 0.7885 (t70) REVERT: A 1537 ASP cc_start: 0.8853 (OUTLIER) cc_final: 0.8400 (p0) REVERT: A 1554 MET cc_start: 0.7737 (tpp) cc_final: 0.7301 (tpt) REVERT: A 1579 PHE cc_start: 0.8828 (t80) cc_final: 0.8605 (t80) REVERT: A 1586 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8605 (mp0) REVERT: A 1594 GLU cc_start: 0.9165 (tt0) cc_final: 0.8521 (tm-30) REVERT: A 1649 ASP cc_start: 0.8900 (t0) cc_final: 0.8390 (t0) REVERT: A 1740 ASP cc_start: 0.8626 (m-30) cc_final: 0.8362 (m-30) REVERT: A 1843 LEU cc_start: 0.7917 (mt) cc_final: 0.7674 (mt) REVERT: A 1874 LYS cc_start: 0.8257 (mttm) cc_final: 0.7741 (mttm) REVERT: A 1890 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.7626 (t80) REVERT: A 1920 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7640 (mt) REVERT: A 2428 LEU cc_start: 0.7278 (mt) cc_final: 0.7033 (mt) REVERT: A 2479 TYR cc_start: 0.7947 (m-10) cc_final: 0.7386 (m-10) REVERT: A 2547 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7955 (tp) REVERT: A 2589 LEU cc_start: 0.8001 (mt) cc_final: 0.7600 (mt) REVERT: A 2595 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.7952 (tp) REVERT: A 2628 LEU cc_start: 0.7644 (mt) cc_final: 0.7373 (mt) REVERT: A 2643 GLU cc_start: 0.6150 (mt-10) cc_final: 0.5828 (mt-10) REVERT: A 2895 ASP cc_start: 0.8044 (m-30) cc_final: 0.7765 (m-30) REVERT: A 2958 LYS cc_start: 0.7910 (mmtt) cc_final: 0.7272 (mmtt) REVERT: A 3098 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7499 (pttt) REVERT: A 3159 ILE cc_start: 0.8077 (mt) cc_final: 0.7570 (pt) REVERT: A 3438 LEU cc_start: 0.8032 (mt) cc_final: 0.7827 (mt) REVERT: A 3443 ASN cc_start: 0.6703 (t0) cc_final: 0.6347 (t160) REVERT: A 3538 ASP cc_start: 0.7852 (t0) cc_final: 0.7406 (t0) REVERT: A 3570 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8194 (ttmm) REVERT: A 3607 ASP cc_start: 0.7007 (m-30) cc_final: 0.6765 (m-30) REVERT: A 3624 LYS cc_start: 0.7718 (tttp) cc_final: 0.7493 (ttpp) REVERT: A 3673 LYS cc_start: 0.7821 (mmtm) cc_final: 0.7388 (mptt) REVERT: A 3711 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8520 (mmmm) REVERT: A 3729 ILE cc_start: 0.7873 (mt) cc_final: 0.7581 (mt) REVERT: B 108 GLU cc_start: 0.7682 (pp20) cc_final: 0.7197 (pp20) REVERT: B 192 LYS cc_start: 0.8027 (ptpp) cc_final: 0.7740 (ptpp) REVERT: B 229 GLN cc_start: 0.7901 (pp30) cc_final: 0.7483 (pt0) REVERT: B 254 GLU cc_start: 0.8097 (mp0) cc_final: 0.7741 (mp0) REVERT: B 297 ASN cc_start: 0.8704 (m-40) cc_final: 0.8400 (m-40) REVERT: B 318 LEU cc_start: 0.8519 (tt) cc_final: 0.8257 (mm) REVERT: G 297 LEU cc_start: 0.7845 (mt) cc_final: 0.7542 (mt) REVERT: G 395 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8427 (mm) REVERT: E 203 ILE cc_start: 0.8510 (mm) cc_final: 0.8200 (mm) REVERT: E 243 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7526 (mt) REVERT: E 253 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7485 (mt) REVERT: E 426 MET cc_start: 0.7279 (tpp) cc_final: 0.6892 (tpp) REVERT: E 467 ASP cc_start: 0.7133 (p0) cc_final: 0.6712 (p0) REVERT: E 480 GLU cc_start: 0.8158 (tt0) cc_final: 0.7891 (tp30) REVERT: E 567 GLU cc_start: 0.7391 (pt0) cc_final: 0.7138 (pt0) REVERT: E 582 ARG cc_start: 0.6928 (mmp80) cc_final: 0.6687 (mmp80) REVERT: E 587 TYR cc_start: 0.6974 (m-80) cc_final: 0.6691 (m-80) REVERT: F 115 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7429 (mt0) REVERT: F 263 ASP cc_start: 0.8309 (t0) cc_final: 0.8078 (t0) REVERT: F 285 ARG cc_start: 0.8454 (ptm160) cc_final: 0.8236 (ptp-170) REVERT: F 337 GLU cc_start: 0.7595 (pt0) cc_final: 0.7347 (pt0) REVERT: C 429 THR cc_start: 0.5844 (t) cc_final: 0.5626 (m) REVERT: C 435 ASN cc_start: 0.7229 (m-40) cc_final: 0.6769 (t0) REVERT: C 439 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7760 (mm-30) REVERT: C 450 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7799 (ttp-110) REVERT: C 652 CYS cc_start: 0.7533 (t) cc_final: 0.7179 (m) outliers start: 151 outliers final: 101 residues processed: 973 average time/residue: 0.5252 time to fit residues: 852.9227 Evaluate side-chains 972 residues out of total 4459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 855 time to evaluate : 4.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 655 GLU Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 748 MET Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 895 GLU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1421 LEU Chi-restraints excluded: chain A residue 1532 ILE Chi-restraints excluded: chain A residue 1537 ASP Chi-restraints excluded: chain A residue 1644 PHE Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1701 GLU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1743 ILE Chi-restraints excluded: chain A residue 1818 SER Chi-restraints excluded: chain A residue 1841 LEU Chi-restraints excluded: chain A residue 1890 TYR Chi-restraints excluded: chain A residue 1920 LEU Chi-restraints excluded: chain A residue 2535 VAL Chi-restraints excluded: chain A residue 2547 LEU Chi-restraints excluded: chain A residue 2595 ILE Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2614 LYS Chi-restraints excluded: chain A residue 2625 VAL Chi-restraints excluded: chain A residue 2669 MET Chi-restraints excluded: chain A residue 2699 ILE Chi-restraints excluded: chain A residue 2729 SER Chi-restraints excluded: chain A residue 2730 LEU Chi-restraints excluded: chain A residue 2742 LEU Chi-restraints excluded: chain A residue 2961 MET Chi-restraints excluded: chain A residue 2963 GLU Chi-restraints excluded: chain A residue 3078 PHE Chi-restraints excluded: chain A residue 3086 CYS Chi-restraints excluded: chain A residue 3098 LYS Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3509 SER Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3533 ILE Chi-restraints excluded: chain A residue 3570 LYS Chi-restraints excluded: chain A residue 3579 LEU Chi-restraints excluded: chain A residue 3584 ILE Chi-restraints excluded: chain A residue 3634 ILE Chi-restraints excluded: chain A residue 3643 ASN Chi-restraints excluded: chain A residue 3661 THR Chi-restraints excluded: chain A residue 3675 HIS Chi-restraints excluded: chain A residue 3718 LEU Chi-restraints excluded: chain A residue 3721 ILE Chi-restraints excluded: chain A residue 3734 SER Chi-restraints excluded: chain A residue 3739 ASP Chi-restraints excluded: chain A residue 3740 MET Chi-restraints excluded: chain A residue 3795 ASN Chi-restraints excluded: chain A residue 3819 SER Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 8 TYR Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 259 GLU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 453 GLU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 497 ASP Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain F residue 298 ASP Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain C residue 450 ARG Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 619 SER Chi-restraints excluded: chain C residue 622 SER Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 459 optimal weight: 6.9990 chunk 53 optimal weight: 0.0010 chunk 271 optimal weight: 0.8980 chunk 348 optimal weight: 0.6980 chunk 269 optimal weight: 1.9990 chunk 401 optimal weight: 10.0000 chunk 266 optimal weight: 2.9990 chunk 475 optimal weight: 0.8980 chunk 297 optimal weight: 0.3980 chunk 289 optimal weight: 0.3980 chunk 219 optimal weight: 0.3980 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 ASN ** A1440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2460 GLN ** A2528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2898 ASN ** A3141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3537 ASN ** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 38654 Z= 0.179 Angle : 0.623 11.215 52497 Z= 0.305 Chirality : 0.040 0.264 6036 Planarity : 0.005 0.054 6755 Dihedral : 5.743 78.634 5377 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.53 % Favored : 96.45 % Rotamer: Outliers : 3.61 % Allowed : 23.51 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.12), residues: 4851 helix: 1.75 (0.10), residues: 3065 sheet: -0.63 (0.36), residues: 190 loop : -0.70 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 87 HIS 0.004 0.001 HIS G 239 PHE 0.032 0.001 PHE A1549 TYR 0.020 0.001 TYR A1872 ARG 0.007 0.000 ARG A2576 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 4459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 888 time to evaluate : 4.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ILE cc_start: 0.9230 (tp) cc_final: 0.8919 (pt) REVERT: A 325 HIS cc_start: 0.7760 (m-70) cc_final: 0.6878 (m-70) REVERT: A 414 LEU cc_start: 0.9208 (tt) cc_final: 0.8954 (tp) REVERT: A 433 GLN cc_start: 0.8491 (mm110) cc_final: 0.8290 (mm-40) REVERT: A 447 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8299 (mtmt) REVERT: A 610 ILE cc_start: 0.9037 (tp) cc_final: 0.8674 (mt) REVERT: A 612 LYS cc_start: 0.8814 (tttt) cc_final: 0.8449 (ttpt) REVERT: A 677 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7665 (tt0) REVERT: A 681 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7184 (mt-10) REVERT: A 686 MET cc_start: 0.6858 (tpp) cc_final: 0.6222 (tpp) REVERT: A 692 ASP cc_start: 0.7134 (p0) cc_final: 0.6827 (p0) REVERT: A 802 GLU cc_start: 0.5946 (OUTLIER) cc_final: 0.5658 (mp0) REVERT: A 865 ASN cc_start: 0.7973 (m-40) cc_final: 0.7716 (m-40) REVERT: A 970 ILE cc_start: 0.8489 (tp) cc_final: 0.8237 (tp) REVERT: A 1023 MET cc_start: 0.7537 (ptt) cc_final: 0.6757 (mtp) REVERT: A 1145 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7391 (tt0) REVERT: A 1335 ASP cc_start: 0.7953 (t0) cc_final: 0.7493 (t0) REVERT: A 1420 ILE cc_start: 0.9040 (tt) cc_final: 0.8818 (tp) REVERT: A 1540 HIS cc_start: 0.8945 (OUTLIER) cc_final: 0.8723 (t70) REVERT: A 1554 MET cc_start: 0.7757 (tpp) cc_final: 0.7317 (tpt) REVERT: A 1579 PHE cc_start: 0.8856 (t80) cc_final: 0.8611 (t80) REVERT: A 1585 ASP cc_start: 0.8607 (p0) cc_final: 0.8160 (p0) REVERT: A 1649 ASP cc_start: 0.8954 (t0) cc_final: 0.8345 (t0) REVERT: A 1650 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8954 (mm) REVERT: A 1740 ASP cc_start: 0.8612 (m-30) cc_final: 0.8327 (m-30) REVERT: A 1843 LEU cc_start: 0.7918 (mt) cc_final: 0.7622 (mt) REVERT: A 1861 MET cc_start: 0.3367 (ptt) cc_final: 0.3080 (ptt) REVERT: A 1874 LYS cc_start: 0.8310 (mttm) cc_final: 0.7826 (mttm) REVERT: A 1890 TYR cc_start: 0.7965 (OUTLIER) cc_final: 0.7676 (t80) REVERT: A 2418 MET cc_start: 0.6517 (mmm) cc_final: 0.5977 (ptm) REVERT: A 2428 LEU cc_start: 0.7356 (mt) cc_final: 0.7088 (mt) REVERT: A 2547 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7994 (tp) REVERT: A 2578 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7847 (tm-30) REVERT: A 2589 LEU cc_start: 0.8024 (mt) cc_final: 0.7600 (mt) REVERT: A 2595 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.7978 (tp) REVERT: A 2628 LEU cc_start: 0.7644 (mt) cc_final: 0.7367 (mt) REVERT: A 2643 GLU cc_start: 0.6140 (mt-10) cc_final: 0.5809 (mt-10) REVERT: A 2895 ASP cc_start: 0.8041 (m-30) cc_final: 0.7759 (m-30) REVERT: A 2958 LYS cc_start: 0.7862 (mmtt) cc_final: 0.7141 (mmtt) REVERT: A 3098 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7496 (pttt) REVERT: A 3159 ILE cc_start: 0.8120 (mt) cc_final: 0.7629 (pt) REVERT: A 3443 ASN cc_start: 0.6689 (t0) cc_final: 0.6292 (t0) REVERT: A 3538 ASP cc_start: 0.7875 (t0) cc_final: 0.7453 (t0) REVERT: A 3570 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8204 (ttmm) REVERT: A 3607 ASP cc_start: 0.7036 (m-30) cc_final: 0.6783 (m-30) REVERT: A 3640 MET cc_start: 0.8189 (mmm) cc_final: 0.7878 (mmm) REVERT: A 3664 MET cc_start: 0.7618 (tpp) cc_final: 0.7402 (tpp) REVERT: A 3673 LYS cc_start: 0.7813 (mmtm) cc_final: 0.7319 (mptt) REVERT: A 3711 LYS cc_start: 0.8786 (mmmt) cc_final: 0.8531 (mmmm) REVERT: A 3726 ILE cc_start: 0.7851 (mt) cc_final: 0.7199 (mm) REVERT: A 3729 ILE cc_start: 0.7864 (mt) cc_final: 0.7561 (mt) REVERT: B 108 GLU cc_start: 0.7681 (pp20) cc_final: 0.7450 (pp20) REVERT: B 192 LYS cc_start: 0.8015 (ptpp) cc_final: 0.7724 (ptpp) REVERT: B 229 GLN cc_start: 0.7914 (pp30) cc_final: 0.7481 (pt0) REVERT: B 254 GLU cc_start: 0.8071 (mp0) cc_final: 0.7749 (mp0) REVERT: B 297 ASN cc_start: 0.8709 (m-40) cc_final: 0.8411 (m-40) REVERT: B 314 MET cc_start: 0.8367 (mmm) cc_final: 0.7838 (tpt) REVERT: B 317 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7486 (mm-30) REVERT: B 318 LEU cc_start: 0.8513 (tt) cc_final: 0.8296 (mm) REVERT: B 362 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7827 (mm-30) REVERT: G 297 LEU cc_start: 0.7809 (mt) cc_final: 0.7512 (mt) REVERT: G 395 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8490 (mm) REVERT: E 203 ILE cc_start: 0.8484 (mm) cc_final: 0.8156 (mm) REVERT: E 243 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7558 (mt) REVERT: E 253 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7527 (mt) REVERT: E 426 MET cc_start: 0.7222 (tpp) cc_final: 0.6848 (tpp) REVERT: E 467 ASP cc_start: 0.7079 (p0) cc_final: 0.6688 (p0) REVERT: E 567 GLU cc_start: 0.7428 (pt0) cc_final: 0.7155 (pt0) REVERT: E 587 TYR cc_start: 0.7006 (m-80) cc_final: 0.6743 (m-80) REVERT: F 115 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7451 (mt0) REVERT: F 321 TYR cc_start: 0.8689 (t80) cc_final: 0.8327 (t80) REVERT: F 338 SER cc_start: 0.9093 (t) cc_final: 0.8681 (p) REVERT: F 362 ARG cc_start: 0.6230 (tpt170) cc_final: 0.6016 (tpt170) REVERT: C 429 THR cc_start: 0.5913 (t) cc_final: 0.5629 (m) REVERT: C 435 ASN cc_start: 0.7166 (m-40) cc_final: 0.6678 (t0) REVERT: C 439 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7796 (mm-30) REVERT: C 450 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7850 (ttp-110) REVERT: C 504 ASP cc_start: 0.8442 (t70) cc_final: 0.7549 (t0) REVERT: C 506 GLU cc_start: 0.7805 (mp0) cc_final: 0.7532 (mp0) REVERT: C 604 MET cc_start: 0.7478 (ptp) cc_final: 0.7252 (ptm) REVERT: C 627 VAL cc_start: 0.9099 (OUTLIER) cc_final: 0.8884 (m) REVERT: C 655 LEU cc_start: 0.7445 (tp) cc_final: 0.7007 (tp) outliers start: 137 outliers final: 83 residues processed: 955 average time/residue: 0.4969 time to fit residues: 790.1841 Evaluate side-chains 934 residues out of total 4459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 835 time to evaluate : 4.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 655 GLU Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 895 GLU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1421 LEU Chi-restraints excluded: chain A residue 1540 HIS Chi-restraints excluded: chain A residue 1644 PHE Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1701 GLU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1820 VAL Chi-restraints excluded: chain A residue 1841 LEU Chi-restraints excluded: chain A residue 1890 TYR Chi-restraints excluded: chain A residue 1913 HIS Chi-restraints excluded: chain A residue 2535 VAL Chi-restraints excluded: chain A residue 2547 LEU Chi-restraints excluded: chain A residue 2595 ILE Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2729 SER Chi-restraints excluded: chain A residue 2730 LEU Chi-restraints excluded: chain A residue 2742 LEU Chi-restraints excluded: chain A residue 2961 MET Chi-restraints excluded: chain A residue 2963 GLU Chi-restraints excluded: chain A residue 3078 PHE Chi-restraints excluded: chain A residue 3086 CYS Chi-restraints excluded: chain A residue 3088 LEU Chi-restraints excluded: chain A residue 3098 LYS Chi-restraints excluded: chain A residue 3172 GLN Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3437 LEU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3570 LYS Chi-restraints excluded: chain A residue 3579 LEU Chi-restraints excluded: chain A residue 3584 ILE Chi-restraints excluded: chain A residue 3614 SER Chi-restraints excluded: chain A residue 3643 ASN Chi-restraints excluded: chain A residue 3661 THR Chi-restraints excluded: chain A residue 3675 HIS Chi-restraints excluded: chain A residue 3734 SER Chi-restraints excluded: chain A residue 3739 ASP Chi-restraints excluded: chain A residue 3740 MET Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 195 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 453 GLU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 497 ASP Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain F residue 298 ASP Chi-restraints excluded: chain C residue 450 ARG Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 619 SER Chi-restraints excluded: chain C residue 627 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 293 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 chunk 283 optimal weight: 0.5980 chunk 143 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 302 optimal weight: 0.9980 chunk 323 optimal weight: 0.0270 chunk 234 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 373 optimal weight: 3.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1769 GLN ** A2528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3537 ASN ** B 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 655 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 38654 Z= 0.205 Angle : 0.635 11.482 52497 Z= 0.311 Chirality : 0.041 0.248 6036 Planarity : 0.005 0.053 6755 Dihedral : 5.701 76.613 5377 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.25 % Rotamer: Outliers : 3.87 % Allowed : 24.12 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.12), residues: 4851 helix: 1.76 (0.10), residues: 3051 sheet: -0.60 (0.35), residues: 190 loop : -0.73 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A2771 HIS 0.005 0.001 HIS G 239 PHE 0.038 0.002 PHE A 702 TYR 0.025 0.001 TYR A1872 ARG 0.007 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 4459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 878 time to evaluate : 4.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ILE cc_start: 0.9166 (tp) cc_final: 0.8878 (pt) REVERT: A 325 HIS cc_start: 0.7761 (m-70) cc_final: 0.6829 (m-70) REVERT: A 447 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8148 (mtmt) REVERT: A 610 ILE cc_start: 0.9024 (tp) cc_final: 0.8676 (mt) REVERT: A 612 LYS cc_start: 0.8811 (tttt) cc_final: 0.8432 (ttpt) REVERT: A 680 ARG cc_start: 0.8413 (tmm-80) cc_final: 0.7915 (ttt-90) REVERT: A 681 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7385 (mt-10) REVERT: A 838 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8043 (mm) REVERT: A 858 LYS cc_start: 0.8524 (tppt) cc_final: 0.7878 (tppt) REVERT: A 865 ASN cc_start: 0.8117 (m-40) cc_final: 0.7856 (m-40) REVERT: A 878 LEU cc_start: 0.8162 (tp) cc_final: 0.7958 (tp) REVERT: A 1023 MET cc_start: 0.7549 (ptt) cc_final: 0.6849 (mtp) REVERT: A 1145 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: A 1156 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7698 (mm-30) REVERT: A 1200 LEU cc_start: 0.7777 (mp) cc_final: 0.7543 (mp) REVERT: A 1335 ASP cc_start: 0.7993 (t0) cc_final: 0.7554 (t0) REVERT: A 1420 ILE cc_start: 0.9074 (tt) cc_final: 0.8863 (tp) REVERT: A 1521 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7652 (pm20) REVERT: A 1522 ASP cc_start: 0.8475 (m-30) cc_final: 0.7648 (t70) REVERT: A 1554 MET cc_start: 0.7710 (tpp) cc_final: 0.7267 (tpt) REVERT: A 1579 PHE cc_start: 0.8859 (t80) cc_final: 0.8613 (t80) REVERT: A 1585 ASP cc_start: 0.8730 (p0) cc_final: 0.8266 (p0) REVERT: A 1649 ASP cc_start: 0.8917 (t0) cc_final: 0.8365 (t0) REVERT: A 1650 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8918 (mm) REVERT: A 1740 ASP cc_start: 0.8590 (m-30) cc_final: 0.8314 (m-30) REVERT: A 1769 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7283 (pm20) REVERT: A 1843 LEU cc_start: 0.7929 (mt) cc_final: 0.7688 (mt) REVERT: A 1861 MET cc_start: 0.3413 (ptt) cc_final: 0.3149 (ptt) REVERT: A 1874 LYS cc_start: 0.8326 (mttm) cc_final: 0.7848 (mttm) REVERT: A 1890 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7828 (t80) REVERT: A 2418 MET cc_start: 0.6599 (mmm) cc_final: 0.5970 (ptm) REVERT: A 2428 LEU cc_start: 0.7438 (mt) cc_final: 0.7175 (mt) REVERT: A 2547 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8030 (tp) REVERT: A 2589 LEU cc_start: 0.8090 (mt) cc_final: 0.7587 (mt) REVERT: A 2595 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.7985 (tp) REVERT: A 2628 LEU cc_start: 0.7731 (mt) cc_final: 0.7496 (mt) REVERT: A 2643 GLU cc_start: 0.6240 (mt-10) cc_final: 0.5877 (mt-10) REVERT: A 2895 ASP cc_start: 0.8149 (m-30) cc_final: 0.7852 (m-30) REVERT: A 2958 LYS cc_start: 0.7857 (mmtt) cc_final: 0.7488 (mmtt) REVERT: A 3098 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7563 (pttt) REVERT: A 3159 ILE cc_start: 0.8154 (mt) cc_final: 0.7608 (pt) REVERT: A 3443 ASN cc_start: 0.6829 (t0) cc_final: 0.6444 (t0) REVERT: A 3607 ASP cc_start: 0.7100 (m-30) cc_final: 0.6815 (m-30) REVERT: A 3640 MET cc_start: 0.8343 (mmm) cc_final: 0.8082 (mmm) REVERT: A 3664 MET cc_start: 0.7706 (tpp) cc_final: 0.7466 (tpp) REVERT: A 3673 LYS cc_start: 0.7802 (mmtm) cc_final: 0.7325 (mptt) REVERT: A 3711 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8576 (mmmm) REVERT: A 3726 ILE cc_start: 0.7870 (mt) cc_final: 0.7279 (mm) REVERT: A 3729 ILE cc_start: 0.7920 (mt) cc_final: 0.7641 (mt) REVERT: B 108 GLU cc_start: 0.7692 (pp20) cc_final: 0.7483 (pp20) REVERT: B 129 ASN cc_start: 0.8330 (t0) cc_final: 0.7650 (t0) REVERT: B 192 LYS cc_start: 0.8027 (ptpp) cc_final: 0.7737 (ptpp) REVERT: B 229 GLN cc_start: 0.7935 (pp30) cc_final: 0.7512 (pt0) REVERT: B 254 GLU cc_start: 0.8087 (mp0) cc_final: 0.7778 (mp0) REVERT: B 297 ASN cc_start: 0.8694 (m-40) cc_final: 0.8393 (m-40) REVERT: B 314 MET cc_start: 0.8371 (mmm) cc_final: 0.7826 (tpt) REVERT: B 317 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7492 (mm-30) REVERT: B 318 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8310 (mm) REVERT: B 347 LEU cc_start: 0.8496 (tp) cc_final: 0.8242 (mm) REVERT: G 201 GLU cc_start: 0.8129 (pm20) cc_final: 0.7364 (pp20) REVERT: G 297 LEU cc_start: 0.7945 (mt) cc_final: 0.7638 (mt) REVERT: G 395 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8488 (mm) REVERT: E 203 ILE cc_start: 0.8557 (mm) cc_final: 0.8217 (mm) REVERT: E 243 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7752 (mp) REVERT: E 249 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6908 (mm-30) REVERT: E 253 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7574 (mt) REVERT: E 426 MET cc_start: 0.7208 (tpp) cc_final: 0.6864 (tpp) REVERT: E 467 ASP cc_start: 0.7104 (p0) cc_final: 0.6720 (p0) REVERT: E 480 GLU cc_start: 0.8259 (tt0) cc_final: 0.7959 (tp30) REVERT: E 567 GLU cc_start: 0.7432 (pt0) cc_final: 0.7157 (pt0) REVERT: E 587 TYR cc_start: 0.7168 (m-80) cc_final: 0.6824 (m-80) REVERT: E 649 GLU cc_start: 0.7822 (pm20) cc_final: 0.7571 (pp20) REVERT: F 115 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7456 (mt0) REVERT: F 321 TYR cc_start: 0.8655 (t80) cc_final: 0.8252 (t80) REVERT: C 429 THR cc_start: 0.5811 (t) cc_final: 0.5598 (m) REVERT: C 435 ASN cc_start: 0.7052 (m-40) cc_final: 0.6549 (t0) REVERT: C 439 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7901 (mm-30) REVERT: C 450 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7811 (ttp-110) REVERT: C 604 MET cc_start: 0.7512 (ptp) cc_final: 0.7203 (ptm) REVERT: C 655 LEU cc_start: 0.7506 (tp) cc_final: 0.7077 (tp) outliers start: 147 outliers final: 98 residues processed: 952 average time/residue: 0.5373 time to fit residues: 859.8273 Evaluate side-chains 970 residues out of total 4459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 856 time to evaluate : 4.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 655 GLU Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 895 GLU Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1421 LEU Chi-restraints excluded: chain A residue 1521 GLN Chi-restraints excluded: chain A residue 1580 LEU Chi-restraints excluded: chain A residue 1644 PHE Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1701 GLU Chi-restraints excluded: chain A residue 1706 LEU Chi-restraints excluded: chain A residue 1769 GLN Chi-restraints excluded: chain A residue 1820 VAL Chi-restraints excluded: chain A residue 1841 LEU Chi-restraints excluded: chain A residue 1890 TYR Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 1913 HIS Chi-restraints excluded: chain A residue 2535 VAL Chi-restraints excluded: chain A residue 2547 LEU Chi-restraints excluded: chain A residue 2595 ILE Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2614 LYS Chi-restraints excluded: chain A residue 2625 VAL Chi-restraints excluded: chain A residue 2669 MET Chi-restraints excluded: chain A residue 2723 PHE Chi-restraints excluded: chain A residue 2729 SER Chi-restraints excluded: chain A residue 2730 LEU Chi-restraints excluded: chain A residue 2742 LEU Chi-restraints excluded: chain A residue 2961 MET Chi-restraints excluded: chain A residue 2963 GLU Chi-restraints excluded: chain A residue 3078 PHE Chi-restraints excluded: chain A residue 3086 CYS Chi-restraints excluded: chain A residue 3088 LEU Chi-restraints excluded: chain A residue 3098 LYS Chi-restraints excluded: chain A residue 3099 THR Chi-restraints excluded: chain A residue 3172 GLN Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3437 LEU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3570 LYS Chi-restraints excluded: chain A residue 3579 LEU Chi-restraints excluded: chain A residue 3584 ILE Chi-restraints excluded: chain A residue 3643 ASN Chi-restraints excluded: chain A residue 3652 ILE Chi-restraints excluded: chain A residue 3661 THR Chi-restraints excluded: chain A residue 3675 HIS Chi-restraints excluded: chain A residue 3721 ILE Chi-restraints excluded: chain A residue 3734 SER Chi-restraints excluded: chain A residue 3739 ASP Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 259 GLU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 438 LEU Chi-restraints excluded: chain G residue 453 GLU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 497 ASP Chi-restraints excluded: chain E residue 504 ILE Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 298 ASP Chi-restraints excluded: chain C residue 431 SER Chi-restraints excluded: chain C residue 450 ARG Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 507 ILE Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 608 ASP Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 432 optimal weight: 0.8980 chunk 455 optimal weight: 0.9990 chunk 415 optimal weight: 0.7980 chunk 442 optimal weight: 0.8980 chunk 266 optimal weight: 0.6980 chunk 192 optimal weight: 8.9990 chunk 347 optimal weight: 0.9980 chunk 135 optimal weight: 7.9990 chunk 400 optimal weight: 3.9990 chunk 418 optimal weight: 0.0980 chunk 441 optimal weight: 0.0070 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3089 GLN ** A3141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3537 ASN G 176 GLN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 655 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 38654 Z= 0.190 Angle : 0.657 16.078 52497 Z= 0.317 Chirality : 0.041 0.240 6036 Planarity : 0.005 0.074 6755 Dihedral : 5.647 73.407 5377 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.65 % Favored : 96.33 % Rotamer: Outliers : 3.53 % Allowed : 24.72 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.12), residues: 4851 helix: 1.75 (0.10), residues: 3043 sheet: -0.29 (0.37), residues: 179 loop : -0.72 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A2771 HIS 0.006 0.001 HIS G 419 PHE 0.028 0.001 PHE A1549 TYR 0.017 0.001 TYR A 563 ARG 0.009 0.000 ARG A1356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 4459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 879 time to evaluate : 4.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ILE cc_start: 0.9196 (tp) cc_final: 0.8913 (pt) REVERT: A 325 HIS cc_start: 0.7761 (m-70) cc_final: 0.6899 (m-70) REVERT: A 330 ILE cc_start: 0.9125 (mm) cc_final: 0.8710 (tp) REVERT: A 350 ARG cc_start: 0.6007 (ttp80) cc_final: 0.5771 (ttp80) REVERT: A 610 ILE cc_start: 0.9012 (tp) cc_final: 0.8687 (mt) REVERT: A 612 LYS cc_start: 0.8805 (tttt) cc_final: 0.8543 (ttpt) REVERT: A 677 GLU cc_start: 0.7786 (tt0) cc_final: 0.6961 (tt0) REVERT: A 680 ARG cc_start: 0.8410 (tmm-80) cc_final: 0.7903 (ttt-90) REVERT: A 681 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7428 (mt-10) REVERT: A 690 MET cc_start: 0.7253 (mpp) cc_final: 0.6842 (mpp) REVERT: A 809 MET cc_start: 0.7559 (ttm) cc_final: 0.7330 (ttp) REVERT: A 838 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8058 (mm) REVERT: A 858 LYS cc_start: 0.8527 (tppt) cc_final: 0.7828 (tppt) REVERT: A 865 ASN cc_start: 0.8175 (m-40) cc_final: 0.7870 (m-40) REVERT: A 975 SER cc_start: 0.8580 (p) cc_final: 0.8348 (m) REVERT: A 1023 MET cc_start: 0.7519 (ptt) cc_final: 0.6810 (mtp) REVERT: A 1058 LEU cc_start: 0.8585 (mt) cc_final: 0.8375 (mt) REVERT: A 1145 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7422 (tt0) REVERT: A 1156 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7718 (mm-30) REVERT: A 1198 MET cc_start: 0.7289 (tmm) cc_final: 0.7022 (tpt) REVERT: A 1200 LEU cc_start: 0.7746 (mp) cc_final: 0.7538 (mp) REVERT: A 1335 ASP cc_start: 0.8062 (t0) cc_final: 0.7662 (t0) REVERT: A 1420 ILE cc_start: 0.9098 (tt) cc_final: 0.8876 (tp) REVERT: A 1521 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7772 (pm20) REVERT: A 1554 MET cc_start: 0.7717 (tpp) cc_final: 0.7252 (tpt) REVERT: A 1579 PHE cc_start: 0.8849 (t80) cc_final: 0.8609 (t80) REVERT: A 1585 ASP cc_start: 0.8717 (p0) cc_final: 0.8266 (p0) REVERT: A 1649 ASP cc_start: 0.8936 (t0) cc_final: 0.8360 (t0) REVERT: A 1650 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8893 (mm) REVERT: A 1740 ASP cc_start: 0.8545 (m-30) cc_final: 0.8301 (m-30) REVERT: A 1861 MET cc_start: 0.3378 (ptt) cc_final: 0.3135 (ptt) REVERT: A 1871 ASN cc_start: 0.8367 (t0) cc_final: 0.8090 (t0) REVERT: A 1874 LYS cc_start: 0.8395 (mttm) cc_final: 0.7998 (mttm) REVERT: A 1890 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.7804 (t80) REVERT: A 2418 MET cc_start: 0.6595 (mmm) cc_final: 0.5918 (ptm) REVERT: A 2428 LEU cc_start: 0.7427 (mt) cc_final: 0.7178 (mt) REVERT: A 2547 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7998 (tp) REVERT: A 2589 LEU cc_start: 0.8130 (mt) cc_final: 0.7606 (mt) REVERT: A 2595 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.7958 (tp) REVERT: A 2628 LEU cc_start: 0.7723 (mt) cc_final: 0.7498 (mt) REVERT: A 2643 GLU cc_start: 0.6276 (mt-10) cc_final: 0.5889 (mt-10) REVERT: A 2895 ASP cc_start: 0.8188 (m-30) cc_final: 0.7876 (m-30) REVERT: A 2958 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7460 (mmtt) REVERT: A 3098 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7552 (pttt) REVERT: A 3443 ASN cc_start: 0.6943 (t0) cc_final: 0.6700 (t0) REVERT: A 3538 ASP cc_start: 0.7980 (t0) cc_final: 0.7593 (t0) REVERT: A 3607 ASP cc_start: 0.7109 (m-30) cc_final: 0.6735 (m-30) REVERT: A 3664 MET cc_start: 0.7735 (tpp) cc_final: 0.7519 (tpp) REVERT: A 3673 LYS cc_start: 0.7802 (mmtm) cc_final: 0.7297 (mptt) REVERT: A 3711 LYS cc_start: 0.8816 (mmmt) cc_final: 0.8598 (mmmm) REVERT: A 3726 ILE cc_start: 0.7837 (mt) cc_final: 0.7301 (mm) REVERT: A 3729 ILE cc_start: 0.7923 (mt) cc_final: 0.7675 (mt) REVERT: B 108 GLU cc_start: 0.7678 (pp20) cc_final: 0.7471 (pp20) REVERT: B 129 ASN cc_start: 0.8331 (t0) cc_final: 0.7677 (t0) REVERT: B 192 LYS cc_start: 0.8054 (ptpp) cc_final: 0.7766 (ptpp) REVERT: B 227 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8168 (tt0) REVERT: B 254 GLU cc_start: 0.8086 (mp0) cc_final: 0.7773 (mp0) REVERT: B 297 ASN cc_start: 0.8679 (m-40) cc_final: 0.8402 (m-40) REVERT: B 314 MET cc_start: 0.8373 (mmm) cc_final: 0.7804 (tpt) REVERT: B 317 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7491 (mm-30) REVERT: B 318 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8313 (mm) REVERT: B 347 LEU cc_start: 0.8468 (tp) cc_final: 0.8242 (mm) REVERT: B 362 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7848 (mm-30) REVERT: G 134 THR cc_start: 0.8263 (t) cc_final: 0.8055 (m) REVERT: G 201 GLU cc_start: 0.8125 (pm20) cc_final: 0.7403 (pp20) REVERT: G 246 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7589 (tt0) REVERT: G 249 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6888 (mt-10) REVERT: G 297 LEU cc_start: 0.7946 (mt) cc_final: 0.7631 (mt) REVERT: G 395 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8511 (mm) REVERT: E 203 ILE cc_start: 0.8561 (mm) cc_final: 0.8246 (mm) REVERT: E 243 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7793 (mp) REVERT: E 253 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7634 (mt) REVERT: E 426 MET cc_start: 0.7208 (tpp) cc_final: 0.6838 (tpp) REVERT: E 467 ASP cc_start: 0.7092 (p0) cc_final: 0.6706 (p0) REVERT: E 567 GLU cc_start: 0.7391 (pt0) cc_final: 0.7115 (pt0) REVERT: E 587 TYR cc_start: 0.7215 (m-80) cc_final: 0.6896 (m-80) REVERT: E 649 GLU cc_start: 0.7824 (pm20) cc_final: 0.7586 (pp20) REVERT: F 115 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7441 (mt0) REVERT: F 321 TYR cc_start: 0.8600 (t80) cc_final: 0.8205 (t80) REVERT: F 362 ARG cc_start: 0.6413 (tpt170) cc_final: 0.6186 (tpt170) REVERT: C 429 THR cc_start: 0.5895 (t) cc_final: 0.5647 (m) REVERT: C 435 ASN cc_start: 0.7002 (m-40) cc_final: 0.6497 (t0) REVERT: C 439 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7856 (mm-30) REVERT: C 504 ASP cc_start: 0.8423 (t70) cc_final: 0.7657 (t0) REVERT: C 573 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7923 (mm-30) REVERT: C 604 MET cc_start: 0.7530 (ptp) cc_final: 0.7180 (ptm) REVERT: C 655 LEU cc_start: 0.7494 (tp) cc_final: 0.7109 (tp) outliers start: 134 outliers final: 99 residues processed: 945 average time/residue: 0.5050 time to fit residues: 794.4703 Evaluate side-chains 961 residues out of total 4459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 849 time to evaluate : 4.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 655 GLU Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 895 GLU Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1421 LEU Chi-restraints excluded: chain A residue 1521 GLN Chi-restraints excluded: chain A residue 1580 LEU Chi-restraints excluded: chain A residue 1644 PHE Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1701 GLU Chi-restraints excluded: chain A residue 1743 ILE Chi-restraints excluded: chain A residue 1813 LEU Chi-restraints excluded: chain A residue 1820 VAL Chi-restraints excluded: chain A residue 1841 LEU Chi-restraints excluded: chain A residue 1890 TYR Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 1913 HIS Chi-restraints excluded: chain A residue 2484 LEU Chi-restraints excluded: chain A residue 2535 VAL Chi-restraints excluded: chain A residue 2547 LEU Chi-restraints excluded: chain A residue 2595 ILE Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2625 VAL Chi-restraints excluded: chain A residue 2723 PHE Chi-restraints excluded: chain A residue 2729 SER Chi-restraints excluded: chain A residue 2730 LEU Chi-restraints excluded: chain A residue 2742 LEU Chi-restraints excluded: chain A residue 2961 MET Chi-restraints excluded: chain A residue 2963 GLU Chi-restraints excluded: chain A residue 3078 PHE Chi-restraints excluded: chain A residue 3086 CYS Chi-restraints excluded: chain A residue 3098 LYS Chi-restraints excluded: chain A residue 3099 THR Chi-restraints excluded: chain A residue 3172 GLN Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3437 LEU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3533 ILE Chi-restraints excluded: chain A residue 3551 GLU Chi-restraints excluded: chain A residue 3570 LYS Chi-restraints excluded: chain A residue 3579 LEU Chi-restraints excluded: chain A residue 3584 ILE Chi-restraints excluded: chain A residue 3643 ASN Chi-restraints excluded: chain A residue 3661 THR Chi-restraints excluded: chain A residue 3675 HIS Chi-restraints excluded: chain A residue 3739 ASP Chi-restraints excluded: chain A residue 3740 MET Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 421 SER Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 453 GLU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 497 ASP Chi-restraints excluded: chain E residue 504 ILE Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 115 GLN Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 298 ASP Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 608 ASP Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 622 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 290 optimal weight: 0.7980 chunk 468 optimal weight: 2.9990 chunk 285 optimal weight: 1.9990 chunk 222 optimal weight: 0.9990 chunk 325 optimal weight: 6.9990 chunk 491 optimal weight: 20.0000 chunk 452 optimal weight: 3.9990 chunk 391 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 302 optimal weight: 0.9980 chunk 239 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 HIS ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2898 ASN ** A3141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3443 ASN A3537 ASN B 253 ASN G 90 ASN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 GLN E 590 ASN E 655 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.6274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 38654 Z= 0.273 Angle : 0.697 16.040 52497 Z= 0.341 Chirality : 0.042 0.240 6036 Planarity : 0.005 0.072 6755 Dihedral : 5.726 73.217 5377 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.14 % Favored : 95.84 % Rotamer: Outliers : 3.34 % Allowed : 25.14 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.12), residues: 4851 helix: 1.67 (0.10), residues: 3039 sheet: -0.23 (0.37), residues: 179 loop : -0.77 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A2771 HIS 0.006 0.001 HIS A2841 PHE 0.029 0.002 PHE A 995 TYR 0.021 0.002 TYR A2696 ARG 0.012 0.001 ARG A3489 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1005 residues out of total 4459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 878 time to evaluate : 4.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ILE cc_start: 0.9183 (tp) cc_final: 0.8921 (pt) REVERT: A 325 HIS cc_start: 0.7870 (m-70) cc_final: 0.7005 (m-70) REVERT: A 330 ILE cc_start: 0.9109 (mm) cc_final: 0.8663 (tp) REVERT: A 350 ARG cc_start: 0.6274 (ttp80) cc_final: 0.5945 (ttp80) REVERT: A 420 GLU cc_start: 0.9121 (tp30) cc_final: 0.8780 (tp30) REVERT: A 539 MET cc_start: 0.7279 (ptp) cc_final: 0.6925 (ptt) REVERT: A 610 ILE cc_start: 0.9038 (tp) cc_final: 0.8721 (mt) REVERT: A 612 LYS cc_start: 0.8822 (tttt) cc_final: 0.8461 (ttpt) REVERT: A 677 GLU cc_start: 0.7846 (tt0) cc_final: 0.7584 (tt0) REVERT: A 680 ARG cc_start: 0.8437 (tmm-80) cc_final: 0.7938 (ttt-90) REVERT: A 681 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7396 (mt-10) REVERT: A 773 LEU cc_start: 0.7180 (mt) cc_final: 0.6543 (tt) REVERT: A 838 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8133 (mm) REVERT: A 858 LYS cc_start: 0.8567 (tppt) cc_final: 0.7854 (tppt) REVERT: A 865 ASN cc_start: 0.8412 (m-40) cc_final: 0.8153 (m-40) REVERT: A 944 LYS cc_start: 0.8265 (mmmt) cc_final: 0.7854 (mmmt) REVERT: A 1023 MET cc_start: 0.7514 (ptt) cc_final: 0.6765 (mtp) REVERT: A 1145 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: A 1253 LYS cc_start: 0.8318 (mptt) cc_final: 0.7993 (mmtm) REVERT: A 1335 ASP cc_start: 0.8149 (t0) cc_final: 0.7788 (t0) REVERT: A 1420 ILE cc_start: 0.9140 (tt) cc_final: 0.8923 (tp) REVERT: A 1521 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7744 (pm20) REVERT: A 1554 MET cc_start: 0.7661 (tpp) cc_final: 0.7265 (tpt) REVERT: A 1579 PHE cc_start: 0.8888 (t80) cc_final: 0.8648 (t80) REVERT: A 1585 ASP cc_start: 0.8719 (p0) cc_final: 0.8303 (p0) REVERT: A 1649 ASP cc_start: 0.8903 (t0) cc_final: 0.8315 (t0) REVERT: A 1650 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8913 (mm) REVERT: A 1735 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.8104 (p90) REVERT: A 1740 ASP cc_start: 0.8567 (m-30) cc_final: 0.8325 (m-30) REVERT: A 1861 MET cc_start: 0.3466 (ptt) cc_final: 0.3242 (ptt) REVERT: A 1874 LYS cc_start: 0.8382 (mttm) cc_final: 0.7909 (mttm) REVERT: A 1890 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.7948 (t80) REVERT: A 2418 MET cc_start: 0.6623 (mmm) cc_final: 0.5872 (ptm) REVERT: A 2428 LEU cc_start: 0.7671 (mt) cc_final: 0.7429 (mt) REVERT: A 2547 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8001 (tp) REVERT: A 2578 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7642 (tm-30) REVERT: A 2589 LEU cc_start: 0.8194 (mt) cc_final: 0.7680 (mt) REVERT: A 2595 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8332 (tp) REVERT: A 2643 GLU cc_start: 0.6453 (mt-10) cc_final: 0.6018 (mt-10) REVERT: A 2842 ILE cc_start: 0.8660 (mt) cc_final: 0.8406 (mp) REVERT: A 2884 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7656 (mm-40) REVERT: A 2895 ASP cc_start: 0.8346 (m-30) cc_final: 0.8040 (m-30) REVERT: A 2958 LYS cc_start: 0.7946 (mmtt) cc_final: 0.7541 (mmtt) REVERT: A 3098 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7640 (pttt) REVERT: A 3443 ASN cc_start: 0.7442 (t0) cc_final: 0.7184 (t0) REVERT: A 3538 ASP cc_start: 0.8143 (t0) cc_final: 0.7808 (t0) REVERT: A 3607 ASP cc_start: 0.7141 (m-30) cc_final: 0.6825 (m-30) REVERT: A 3673 LYS cc_start: 0.7755 (mmtm) cc_final: 0.7265 (mptt) REVERT: A 3711 LYS cc_start: 0.8856 (mmmt) cc_final: 0.8637 (mmmm) REVERT: A 3726 ILE cc_start: 0.7891 (mt) cc_final: 0.7396 (mm) REVERT: B 108 GLU cc_start: 0.7627 (pp20) cc_final: 0.7327 (pp20) REVERT: B 129 ASN cc_start: 0.8325 (t0) cc_final: 0.7676 (t0) REVERT: B 192 LYS cc_start: 0.8117 (ptpp) cc_final: 0.7836 (ptpp) REVERT: B 226 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8633 (mm-40) REVERT: B 229 GLN cc_start: 0.7907 (pp30) cc_final: 0.7506 (pt0) REVERT: B 254 GLU cc_start: 0.8149 (mp0) cc_final: 0.7854 (mp0) REVERT: B 297 ASN cc_start: 0.8733 (m-40) cc_final: 0.8494 (m-40) REVERT: B 314 MET cc_start: 0.8447 (mmm) cc_final: 0.7983 (tpt) REVERT: B 317 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7524 (mm-30) REVERT: G 134 THR cc_start: 0.8304 (t) cc_final: 0.8092 (m) REVERT: G 201 GLU cc_start: 0.8117 (pm20) cc_final: 0.7418 (pp20) REVERT: G 297 LEU cc_start: 0.8190 (mt) cc_final: 0.7847 (mt) REVERT: G 395 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8571 (mm) REVERT: E 200 LYS cc_start: 0.8415 (ttpt) cc_final: 0.8199 (ttpt) REVERT: E 243 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7981 (mt) REVERT: E 249 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6963 (mm-30) REVERT: E 253 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7750 (mt) REVERT: E 417 ILE cc_start: 0.8181 (tt) cc_final: 0.7951 (tt) REVERT: E 426 MET cc_start: 0.7185 (tpp) cc_final: 0.6878 (tpp) REVERT: E 467 ASP cc_start: 0.7103 (p0) cc_final: 0.6737 (p0) REVERT: E 587 TYR cc_start: 0.7504 (m-80) cc_final: 0.7273 (m-80) REVERT: E 649 GLU cc_start: 0.7827 (pm20) cc_final: 0.7585 (pp20) REVERT: F 104 LYS cc_start: 0.7582 (mmtt) cc_final: 0.7344 (mmmt) REVERT: F 253 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8288 (tttt) REVERT: F 321 TYR cc_start: 0.8611 (t80) cc_final: 0.8206 (t80) REVERT: F 362 ARG cc_start: 0.6530 (tpt170) cc_final: 0.6300 (tpt170) REVERT: C 429 THR cc_start: 0.5791 (t) cc_final: 0.5581 (m) REVERT: C 617 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8057 (mm) REVERT: C 652 CYS cc_start: 0.7505 (t) cc_final: 0.7197 (m) REVERT: C 655 LEU cc_start: 0.7642 (tp) cc_final: 0.7302 (tp) outliers start: 127 outliers final: 94 residues processed: 942 average time/residue: 0.5102 time to fit residues: 799.8157 Evaluate side-chains 945 residues out of total 4459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 838 time to evaluate : 4.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 382 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 655 GLU Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 895 GLU Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1063 GLU Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1268 LEU Chi-restraints excluded: chain A residue 1421 LEU Chi-restraints excluded: chain A residue 1521 GLN Chi-restraints excluded: chain A residue 1580 LEU Chi-restraints excluded: chain A residue 1644 PHE Chi-restraints excluded: chain A residue 1650 LEU Chi-restraints excluded: chain A residue 1682 LEU Chi-restraints excluded: chain A residue 1701 GLU Chi-restraints excluded: chain A residue 1735 PHE Chi-restraints excluded: chain A residue 1743 ILE Chi-restraints excluded: chain A residue 1813 LEU Chi-restraints excluded: chain A residue 1820 VAL Chi-restraints excluded: chain A residue 1841 LEU Chi-restraints excluded: chain A residue 1890 TYR Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 2484 LEU Chi-restraints excluded: chain A residue 2535 VAL Chi-restraints excluded: chain A residue 2547 LEU Chi-restraints excluded: chain A residue 2595 ILE Chi-restraints excluded: chain A residue 2607 SER Chi-restraints excluded: chain A residue 2625 VAL Chi-restraints excluded: chain A residue 2723 PHE Chi-restraints excluded: chain A residue 2729 SER Chi-restraints excluded: chain A residue 2742 LEU Chi-restraints excluded: chain A residue 2961 MET Chi-restraints excluded: chain A residue 2963 GLU Chi-restraints excluded: chain A residue 3078 PHE Chi-restraints excluded: chain A residue 3086 CYS Chi-restraints excluded: chain A residue 3098 LYS Chi-restraints excluded: chain A residue 3099 THR Chi-restraints excluded: chain A residue 3172 GLN Chi-restraints excluded: chain A residue 3307 LEU Chi-restraints excluded: chain A residue 3420 SER Chi-restraints excluded: chain A residue 3437 LEU Chi-restraints excluded: chain A residue 3512 VAL Chi-restraints excluded: chain A residue 3533 ILE Chi-restraints excluded: chain A residue 3551 GLU Chi-restraints excluded: chain A residue 3570 LYS Chi-restraints excluded: chain A residue 3579 LEU Chi-restraints excluded: chain A residue 3584 ILE Chi-restraints excluded: chain A residue 3643 ASN Chi-restraints excluded: chain A residue 3661 THR Chi-restraints excluded: chain A residue 3675 HIS Chi-restraints excluded: chain A residue 3739 ASP Chi-restraints excluded: chain A residue 3740 MET Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 142 CYS Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 259 GLU Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 395 LEU Chi-restraints excluded: chain G residue 438 LEU Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 453 GLU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 504 ILE Chi-restraints excluded: chain E residue 646 VAL Chi-restraints excluded: chain E residue 679 ARG Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 566 ASP Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 622 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 310 optimal weight: 1.9990 chunk 416 optimal weight: 8.9990 chunk 119 optimal weight: 0.6980 chunk 360 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 391 optimal weight: 0.5980 chunk 163 optimal weight: 0.9990 chunk 402 optimal weight: 0.0570 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1555 ASN ** A1769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2898 ASN ** A3141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3537 ASN A3596 GLN B 253 ASN E 590 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.171247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.129068 restraints weight = 73953.313| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.78 r_work: 0.3531 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.6476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 38654 Z= 0.204 Angle : 0.681 15.896 52497 Z= 0.330 Chirality : 0.041 0.239 6036 Planarity : 0.005 0.085 6755 Dihedral : 5.660 72.857 5377 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.63 % Favored : 96.35 % Rotamer: Outliers : 3.08 % Allowed : 26.07 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.12), residues: 4851 helix: 1.69 (0.10), residues: 3037 sheet: -0.21 (0.37), residues: 179 loop : -0.76 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP E 499 HIS 0.005 0.001 HIS A 920 PHE 0.030 0.002 PHE A1604 TYR 0.017 0.001 TYR A 687 ARG 0.011 0.000 ARG A2881 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14364.00 seconds wall clock time: 256 minutes 42.16 seconds (15402.16 seconds total)