Starting phenix.real_space_refine on Fri Feb 6 08:01:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9syu_55354/02_2026/9syu_55354.cif Found real_map, /net/cci-nas-00/data/ceres_data/9syu_55354/02_2026/9syu_55354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9syu_55354/02_2026/9syu_55354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9syu_55354/02_2026/9syu_55354.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9syu_55354/02_2026/9syu_55354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9syu_55354/02_2026/9syu_55354.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 4 5.21 5 S 146 5.16 5 C 14761 2.51 5 N 4066 2.21 5 O 4556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 161 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23539 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 917, 7435 Classifications: {'peptide': 917} Link IDs: {'PTRANS': 30, 'TRANS': 886} Chain breaks: 1 Chain: "B" Number of atoms: 7415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 7415 Classifications: {'peptide': 915} Link IDs: {'PTRANS': 30, 'TRANS': 884} Chain breaks: 1 Chain: "C" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1174 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 3, 'TRANS': 146} Chain: "D" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1175 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 146} Chain: "E" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1229 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 5, 'TRANS': 146} Chain: "F" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1281 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain: "G" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1881 Classifications: {'peptide': 229} Link IDs: {'TRANS': 228} Chain: "H" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1881 Classifications: {'peptide': 229} Link IDs: {'TRANS': 228} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.48, per 1000 atoms: 0.19 Number of scatterers: 23539 At special positions: 0 Unit cell: (97.58, 172.2, 215.66, 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 146 16.00 P 6 15.00 Mg 4 11.99 O 4556 8.00 N 4066 7.00 C 14761 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 - 3.00 Amino acid : True - 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: 1.68 Conformation dependent library (CDL) restraints added in 739.9 milliseconds 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5508 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 15 sheets defined 67.6% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 removed outlier: 4.015A pdb=" N LYS A 8 " --> pdb=" O GLN A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 18 removed outlier: 4.214A pdb=" N PHE A 16 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 18 " --> pdb=" O ASN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 30 removed outlier: 3.957A pdb=" N GLN A 23 " --> pdb=" O ASN A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 93 through 107 Processing helix chain 'A' and resid 131 through 139 Processing helix chain 'A' and resid 149 through 165 Processing helix chain 'A' and resid 179 through 195 Processing helix chain 'A' and resid 205 through 223 removed outlier: 3.559A pdb=" N GLN A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASN A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 260 through 265 Processing helix chain 'A' and resid 274 through 284 removed outlier: 4.199A pdb=" N TYR A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 314 through 330 removed outlier: 3.666A pdb=" N GLN A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 349 Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 406 through 438 Processing helix chain 'A' and resid 463 through 486 Processing helix chain 'A' and resid 486 through 495 Processing helix chain 'A' and resid 508 through 517 Processing helix chain 'A' and resid 523 through 532 Processing helix chain 'A' and resid 538 through 550 Processing helix chain 'A' and resid 583 through 590 Processing helix chain 'A' and resid 593 through 602 Processing helix chain 'A' and resid 605 through 612 Processing helix chain 'A' and resid 645 through 664 Processing helix chain 'A' and resid 684 through 696 Processing helix chain 'A' and resid 696 through 707 Processing helix chain 'A' and resid 714 through 722 Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 735 through 748 Processing helix chain 'A' and resid 766 through 823 removed outlier: 3.961A pdb=" N ASP A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS A 821 " --> pdb=" O ALA A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 839 Proline residue: A 836 - end of helix Processing helix chain 'A' and resid 844 through 931 removed outlier: 3.801A pdb=" N MET A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 13 through 18 Processing helix chain 'B' and resid 19 through 30 removed outlier: 3.924A pdb=" N GLN B 23 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TRP B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 85 through 89 Processing helix chain 'B' and resid 93 through 107 Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.637A pdb=" N MET B 146 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 165 Processing helix chain 'B' and resid 179 through 198 Processing helix chain 'B' and resid 205 through 221 removed outlier: 4.041A pdb=" N LEU B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 274 through 282 removed outlier: 4.147A pdb=" N TYR B 278 " --> pdb=" O PHE B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 293 Processing helix chain 'B' and resid 296 through 300 Processing helix chain 'B' and resid 314 through 329 removed outlier: 3.549A pdb=" N GLN B 320 " --> pdb=" O LYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 350 Processing helix chain 'B' and resid 368 through 379 Processing helix chain 'B' and resid 381 through 391 Processing helix chain 'B' and resid 406 through 438 Processing helix chain 'B' and resid 463 through 496 removed outlier: 3.991A pdb=" N LEU B 487 " --> pdb=" O THR B 483 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU B 488 " --> pdb=" O MET B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 517 Processing helix chain 'B' and resid 523 through 530 Processing helix chain 'B' and resid 538 through 550 Processing helix chain 'B' and resid 583 through 590 Processing helix chain 'B' and resid 593 through 602 Processing helix chain 'B' and resid 605 through 612 Processing helix chain 'B' and resid 614 through 618 removed outlier: 3.890A pdb=" N ARG B 617 " --> pdb=" O ASP B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 662 Processing helix chain 'B' and resid 684 through 696 Processing helix chain 'B' and resid 696 through 707 Processing helix chain 'B' and resid 714 through 722 Processing helix chain 'B' and resid 723 through 725 No H-bonds generated for 'chain 'B' and resid 723 through 725' Processing helix chain 'B' and resid 735 through 747 Processing helix chain 'B' and resid 766 through 826 removed outlier: 4.252A pdb=" N MET B 809 " --> pdb=" O GLN B 805 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL B 811 " --> pdb=" O THR B 807 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG B 814 " --> pdb=" O LYS B 810 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP B 825 " --> pdb=" O LYS B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 838 removed outlier: 3.722A pdb=" N PHE B 831 " --> pdb=" O TRP B 827 " (cutoff:3.500A) Proline residue: B 836 - end of helix Processing helix chain 'B' and resid 838 through 931 removed outlier: 4.061A pdb=" N ARG B 842 " --> pdb=" O LEU B 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 17 removed outlier: 3.786A pdb=" N GLU C 10 " --> pdb=" O GLU C 6 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU C 13 " --> pdb=" O ALA C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 38 removed outlier: 4.273A pdb=" N GLY C 32 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASP C 33 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 51 Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 66 through 79 Proline residue: C 71 - end of helix Processing helix chain 'C' and resid 84 through 93 removed outlier: 3.974A pdb=" N GLU C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 105 through 115 Processing helix chain 'C' and resid 120 through 129 Processing helix chain 'C' and resid 139 through 150 Processing helix chain 'D' and resid 4 through 18 removed outlier: 4.377A pdb=" N GLU D 10 " --> pdb=" O GLU D 6 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU D 13 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU D 17 " --> pdb=" O GLU D 13 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE D 18 " --> pdb=" O ALA D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 38 removed outlier: 3.563A pdb=" N GLY D 32 " --> pdb=" O TYR D 28 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP D 33 " --> pdb=" O SER D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'D' and resid 66 through 78 Proline residue: D 71 - end of helix Processing helix chain 'D' and resid 84 through 94 Processing helix chain 'D' and resid 104 through 115 removed outlier: 3.976A pdb=" N ILE D 108 " --> pdb=" O MET D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 139 through 148 removed outlier: 3.858A pdb=" N LEU D 143 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 26 through 41 Processing helix chain 'E' and resid 49 through 61 Processing helix chain 'E' and resid 66 through 68 No H-bonds generated for 'chain 'E' and resid 66 through 68' Processing helix chain 'E' and resid 69 through 74 Processing helix chain 'E' and resid 81 through 94 removed outlier: 3.773A pdb=" N LYS E 92 " --> pdb=" O MET E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 108 removed outlier: 3.749A pdb=" N CYS E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 129 removed outlier: 3.827A pdb=" N MET E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 143 Processing helix chain 'E' and resid 154 through 162 removed outlier: 3.541A pdb=" N ARG E 160 " --> pdb=" O ILE E 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 25 Processing helix chain 'F' and resid 26 through 41 Processing helix chain 'F' and resid 49 through 60 Processing helix chain 'F' and resid 65 through 76 removed outlier: 4.028A pdb=" N LEU F 69 " --> pdb=" O THR F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 94 removed outlier: 3.692A pdb=" N LYS F 92 " --> pdb=" O MET F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 110 Processing helix chain 'F' and resid 118 through 128 Processing helix chain 'F' and resid 134 through 145 removed outlier: 3.599A pdb=" N LEU F 141 " --> pdb=" O GLU F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 164 Processing helix chain 'G' and resid 1392 through 1513 removed outlier: 3.715A pdb=" N LEU G1397 " --> pdb=" O ASP G1393 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS G1413 " --> pdb=" O ASP G1409 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR G1414 " --> pdb=" O LYS G1410 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASP G1447 " --> pdb=" O GLN G1443 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLN G1448 " --> pdb=" O LYS G1444 " (cutoff:3.500A) Processing helix chain 'G' and resid 1514 through 1617 Processing helix chain 'G' and resid 1618 through 1619 No H-bonds generated for 'chain 'G' and resid 1618 through 1619' Processing helix chain 'H' and resid 1391 through 1392 No H-bonds generated for 'chain 'H' and resid 1391 through 1392' Processing helix chain 'H' and resid 1393 through 1510 removed outlier: 3.673A pdb=" N GLN H1434 " --> pdb=" O ASP H1430 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU H1439 " --> pdb=" O SER H1435 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LYS H1442 " --> pdb=" O ASN H1438 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS H1445 " --> pdb=" O LYS H1441 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR H1476 " --> pdb=" O ARG H1472 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR H1504 " --> pdb=" O LYS H1500 " (cutoff:3.500A) Processing helix chain 'H' and resid 1519 through 1617 removed outlier: 4.100A pdb=" N ASP H1546 " --> pdb=" O GLU H1542 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU H1597 " --> pdb=" O GLU H1593 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS H1603 " --> pdb=" O GLU H1599 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET H1617 " --> pdb=" O LYS H1613 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 111 through 114 removed outlier: 6.768A pdb=" N CYS A 118 " --> pdb=" O ARG A 670 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE A 672 " --> pdb=" O CYS A 118 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL A 120 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N SER A 169 " --> pdb=" O ASN A 667 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL A 669 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU A 171 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N CYS A 671 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR A 173 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLN A 168 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU A 451 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE A 170 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY A 251 " --> pdb=" O ASN A 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 355 through 356 Processing sheet with id=AA4, first strand: chain 'A' and resid 393 through 396 Processing sheet with id=AA5, first strand: chain 'A' and resid 556 through 557 Processing sheet with id=AA6, first strand: chain 'A' and resid 710 through 713 Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 68 removed outlier: 6.947A pdb=" N GLU B 53 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU B 49 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE B 55 " --> pdb=" O LYS B 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 111 through 113 removed outlier: 6.684A pdb=" N CYS B 118 " --> pdb=" O ARG B 670 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE B 672 " --> pdb=" O CYS B 118 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 120 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER B 169 " --> pdb=" O ASN B 667 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL B 669 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU B 171 " --> pdb=" O VAL B 669 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N CYS B 671 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N THR B 173 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN B 168 " --> pdb=" O GLY B 449 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LEU B 451 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE B 170 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 251 " --> pdb=" O ASN B 242 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 393 through 396 Processing sheet with id=AB1, first strand: chain 'B' and resid 556 through 557 removed outlier: 3.687A pdb=" N CYS B 569 " --> pdb=" O GLN B 557 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 710 through 713 Processing sheet with id=AB3, first strand: chain 'C' and resid 25 through 27 Processing sheet with id=AB4, first strand: chain 'C' and resid 103 through 104 Processing sheet with id=AB5, first strand: chain 'D' and resid 25 through 27 Processing sheet with id=AB6, first strand: chain 'E' and resid 117 through 118 1544 hydrogen bonds defined for protein. 4506 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: 3.93 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7741 1.34 - 1.46: 3797 1.46 - 1.58: 12106 1.58 - 1.70: 6 1.70 - 1.82: 246 Bond restraints: 23896 Sorted by residual: bond pdb=" CG1 ILE B 497 " pdb=" CD1 ILE B 497 " ideal model delta sigma weight residual 1.513 1.411 0.102 3.90e-02 6.57e+02 6.90e+00 bond pdb=" CZ ARG G1528 " pdb=" NH2 ARG G1528 " ideal model delta sigma weight residual 1.330 1.301 0.029 1.30e-02 5.92e+03 4.86e+00 bond pdb=" N LYS A 441 " pdb=" CA LYS A 441 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.54e-02 4.22e+03 4.59e+00 bond pdb=" CD2 HIS G1521 " pdb=" NE2 HIS G1521 " ideal model delta sigma weight residual 1.374 1.397 -0.023 1.10e-02 8.26e+03 4.53e+00 bond pdb=" CE1 HIS G1521 " pdb=" NE2 HIS G1521 " ideal model delta sigma weight residual 1.321 1.342 -0.021 1.00e-02 1.00e+04 4.48e+00 ... (remaining 23891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 31165 2.14 - 4.28: 815 4.28 - 6.42: 86 6.42 - 8.56: 19 8.56 - 10.70: 4 Bond angle restraints: 32089 Sorted by residual: angle pdb=" N ALA A 537 " pdb=" CA ALA A 537 " pdb=" C ALA A 537 " ideal model delta sigma weight residual 109.24 117.69 -8.45 1.51e+00 4.39e-01 3.13e+01 angle pdb=" N PHE A 534 " pdb=" CA PHE A 534 " pdb=" C PHE A 534 " ideal model delta sigma weight residual 109.81 119.87 -10.06 2.21e+00 2.05e-01 2.07e+01 angle pdb=" C ALA A 537 " pdb=" N THR A 538 " pdb=" CA THR A 538 " ideal model delta sigma weight residual 122.36 128.85 -6.49 1.60e+00 3.91e-01 1.65e+01 angle pdb=" CA PHE A 534 " pdb=" C PHE A 534 " pdb=" N PRO A 535 " ideal model delta sigma weight residual 118.44 124.70 -6.26 1.59e+00 3.96e-01 1.55e+01 angle pdb=" CA ILE B 497 " pdb=" CB ILE B 497 " pdb=" CG2 ILE B 497 " ideal model delta sigma weight residual 110.50 117.13 -6.63 1.70e+00 3.46e-01 1.52e+01 ... (remaining 32084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.70: 14217 27.70 - 55.40: 499 55.40 - 83.10: 91 83.10 - 110.80: 18 110.80 - 138.50: 1 Dihedral angle restraints: 14826 sinusoidal: 6350 harmonic: 8476 Sorted by residual: dihedral pdb=" O1B ADP A2001 " pdb=" O3A ADP A2001 " pdb=" PB ADP A2001 " pdb=" PA ADP A2001 " ideal model delta sinusoidal sigma weight residual 300.00 161.50 138.50 1 2.00e+01 2.50e-03 4.20e+01 dihedral pdb=" CA PHE B 354 " pdb=" C PHE B 354 " pdb=" N LYS B 355 " pdb=" CA LYS B 355 " ideal model delta harmonic sigma weight residual -180.00 -151.12 -28.88 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA LYS A 536 " pdb=" C LYS A 536 " pdb=" N ALA A 537 " pdb=" CA ALA A 537 " ideal model delta harmonic sigma weight residual -180.00 -151.52 -28.48 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 14823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2978 0.059 - 0.118: 420 0.118 - 0.177: 63 0.177 - 0.236: 10 0.236 - 0.295: 2 Chirality restraints: 3473 Sorted by residual: chirality pdb=" CA PHE A 534 " pdb=" N PHE A 534 " pdb=" C PHE A 534 " pdb=" CB PHE A 534 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA LEU G1509 " pdb=" N LEU G1509 " pdb=" C LEU G1509 " pdb=" CB LEU G1509 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA ASN F 63 " pdb=" N ASN F 63 " pdb=" C ASN F 63 " pdb=" CB ASN F 63 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 3470 not shown) Planarity restraints: 4217 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS G1521 " -0.027 2.00e-02 2.50e+03 2.12e-02 6.72e+00 pdb=" CG HIS G1521 " 0.041 2.00e-02 2.50e+03 pdb=" ND1 HIS G1521 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS G1521 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS G1521 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS G1521 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 263 " 0.227 9.50e-02 1.11e+02 1.02e-01 6.41e+00 pdb=" NE ARG A 263 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 263 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 263 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 263 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 129 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C ILE B 129 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE B 129 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR B 130 " 0.013 2.00e-02 2.50e+03 ... (remaining 4214 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.38: 21 2.38 - 3.01: 12842 3.01 - 3.64: 36349 3.64 - 4.27: 53361 4.27 - 4.90: 88979 Nonbonded interactions: 191552 Sorted by model distance: nonbonded pdb=" O4 PO4 B2002 " pdb="MG MG B2003 " model vdw 1.756 2.170 nonbonded pdb=" OD1 ASN F 43 " pdb="MG MG F9000 " model vdw 1.857 2.170 nonbonded pdb=" OD1 ASP F 41 " pdb="MG MG F9000 " model vdw 1.884 2.170 nonbonded pdb=" O2B ADP B2001 " pdb="MG MG B2003 " model vdw 1.892 2.170 nonbonded pdb=" OD1 ASP E 41 " pdb="MG MG E9000 " model vdw 1.926 2.170 ... (remaining 191547 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 623 or resid 640 through 2003)) selection = (chain 'B' and (resid 2 through 623 or resid 640 through 2003)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 1 through 149 or (resid 150 and (name N or name CA or name \ C or name O )))) } ncs_group { reference = chain 'E' selection = (chain 'F' and resid 16 through 9000) } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 8.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.420 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 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 : 0.005 0.102 23896 Z= 0.283 Angle : 0.801 10.699 32089 Z= 0.458 Chirality : 0.043 0.295 3473 Planarity : 0.007 0.102 4217 Dihedral : 15.134 138.496 9318 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 1.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.20 % Allowed : 5.44 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 2880 helix: 0.23 (0.11), residues: 1810 sheet: -0.10 (0.37), residues: 190 loop : -0.70 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 705 TYR 0.033 0.002 TYR B 422 PHE 0.036 0.003 PHE B 80 TRP 0.016 0.003 TRP A 33 HIS 0.014 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00521 (23896) covalent geometry : angle 0.80107 (32089) hydrogen bonds : bond 0.10482 ( 1544) hydrogen bonds : angle 5.54992 ( 4506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 766 time to evaluate : 0.793 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 538 THR cc_start: 0.8896 (p) cc_final: 0.8581 (t) REVERT: A 752 ASN cc_start: 0.7776 (t0) cc_final: 0.7332 (t0) REVERT: A 838 LEU cc_start: 0.7224 (pp) cc_final: 0.5923 (pp) REVERT: B 92 LEU cc_start: 0.7860 (tt) cc_final: 0.7588 (tt) REVERT: B 434 ASN cc_start: 0.7629 (m-40) cc_final: 0.7407 (m110) REVERT: B 831 PHE cc_start: 0.5472 (t80) cc_final: 0.4858 (t80) REVERT: C 28 TYR cc_start: 0.7108 (m-10) cc_final: 0.6872 (m-10) REVERT: E 49 ASP cc_start: 0.4289 (p0) cc_final: 0.4055 (p0) REVERT: G 1430 ASP cc_start: 0.7646 (t70) cc_final: 0.7341 (t70) outliers start: 5 outliers final: 4 residues processed: 767 average time/residue: 0.7034 time to fit residues: 603.4518 Evaluate side-chains 625 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 621 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain B residue 497 ILE Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain G residue 1607 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 73 GLN A 163 GLN A 246 ASN A 275 HIS A 313 GLN A 402 GLN A 405 GLN A 500 ASN ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 189 GLN B 572 HIS B 758 GLN B 803 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 890 GLN C 126 GLN F 54 HIS F 152 ASN G1434 GLN G1438 ASN G1499 ASN G1521 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.182122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.143939 restraints weight = 47265.207| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.99 r_work: 0.3658 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 23896 Z= 0.242 Angle : 0.757 11.223 32089 Z= 0.390 Chirality : 0.045 0.297 3473 Planarity : 0.005 0.076 4217 Dihedral : 7.100 152.523 3158 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.59 % Allowed : 16.19 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.15), residues: 2880 helix: 1.09 (0.11), residues: 1826 sheet: -0.10 (0.35), residues: 194 loop : -0.33 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 143 TYR 0.022 0.002 TYR A 422 PHE 0.028 0.003 PHE F 47 TRP 0.026 0.003 TRP B 828 HIS 0.007 0.002 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00572 (23896) covalent geometry : angle 0.75689 (32089) hydrogen bonds : bond 0.04975 ( 1544) hydrogen bonds : angle 4.58275 ( 4506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 652 time to evaluate : 0.889 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: 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 9 TYR cc_start: 0.7836 (m-80) cc_final: 0.7530 (m-80) REVERT: A 141 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8357 (mmtm) REVERT: A 316 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8188 (mptt) REVERT: A 324 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: A 327 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7823 (ttp80) REVERT: A 401 VAL cc_start: 0.8707 (m) cc_final: 0.8311 (t) REVERT: A 402 GLN cc_start: 0.8337 (mm-40) cc_final: 0.8137 (mp-120) REVERT: A 498 GLU cc_start: 0.7138 (pp20) cc_final: 0.6625 (pp20) REVERT: A 544 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7860 (mm-30) REVERT: A 548 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7464 (mp10) REVERT: A 549 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7380 (tm-30) REVERT: A 558 LYS cc_start: 0.8457 (mppt) cc_final: 0.8222 (mppt) REVERT: A 662 ARG cc_start: 0.8712 (mtm-85) cc_final: 0.8396 (mtt-85) REVERT: A 752 ASN cc_start: 0.8588 (t0) cc_final: 0.8258 (t0) REVERT: A 802 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8189 (ttm-80) REVERT: A 814 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.8001 (ptt90) REVERT: A 821 LYS cc_start: 0.7841 (pptt) cc_final: 0.7304 (ptmm) REVERT: A 829 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8040 (pmm-80) REVERT: B 125 LYS cc_start: 0.8549 (mttt) cc_final: 0.8322 (mptt) REVERT: B 146 MET cc_start: 0.8093 (mmp) cc_final: 0.7842 (mmt) REVERT: B 164 ASP cc_start: 0.8389 (m-30) cc_final: 0.8186 (m-30) REVERT: B 324 GLU cc_start: 0.6857 (tm-30) cc_final: 0.6557 (tm-30) REVERT: B 516 GLU cc_start: 0.7215 (pt0) cc_final: 0.6968 (pt0) REVERT: B 517 LYS cc_start: 0.8357 (ttpt) cc_final: 0.8012 (tttp) REVERT: B 540 LYS cc_start: 0.6191 (OUTLIER) cc_final: 0.5586 (tmmm) REVERT: B 583 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7451 (mm-30) REVERT: B 783 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7093 (mt) REVERT: B 805 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7201 (mm-40) REVERT: B 829 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8147 (ptm-80) REVERT: C 48 MET cc_start: 0.8427 (mmp) cc_final: 0.8138 (mmp) REVERT: C 59 MET cc_start: 0.7155 (mmm) cc_final: 0.6864 (mmm) REVERT: C 70 LEU cc_start: 0.8396 (tm) cc_final: 0.8122 (tt) REVERT: C 119 MET cc_start: 0.9150 (mtp) cc_final: 0.8937 (mtp) REVERT: D 11 PHE cc_start: 0.8650 (m-10) cc_final: 0.8426 (m-10) REVERT: D 35 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7348 (tpt) REVERT: D 72 MET cc_start: 0.7607 (tpt) cc_final: 0.7175 (ttp) REVERT: E 72 MET cc_start: 0.6698 (ttm) cc_final: 0.6381 (ttm) REVERT: E 80 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7649 (pp) REVERT: E 102 ILE cc_start: 0.8975 (mm) cc_final: 0.8753 (mp) REVERT: E 157 GLU cc_start: 0.7806 (tp30) cc_final: 0.7573 (tp30) REVERT: F 39 MET cc_start: 0.6089 (OUTLIER) cc_final: 0.5888 (mtt) REVERT: F 49 ASP cc_start: 0.7689 (t0) cc_final: 0.7415 (t70) REVERT: F 53 LEU cc_start: 0.8715 (tp) cc_final: 0.8395 (tp) REVERT: F 56 MET cc_start: 0.8423 (tmm) cc_final: 0.8005 (mmm) REVERT: F 62 LYS cc_start: 0.5285 (OUTLIER) cc_final: 0.5008 (mmtt) REVERT: F 63 ASN cc_start: 0.7878 (m110) cc_final: 0.7603 (p0) REVERT: F 84 MET cc_start: 0.6040 (ttm) cc_final: 0.5759 (ttm) REVERT: F 88 MET cc_start: 0.6514 (ttt) cc_final: 0.6064 (ttt) REVERT: F 89 PHE cc_start: 0.5809 (OUTLIER) cc_final: 0.4772 (t80) REVERT: F 100 ASP cc_start: 0.6819 (p0) cc_final: 0.6417 (p0) REVERT: F 110 ASP cc_start: 0.4511 (t70) cc_final: 0.3740 (p0) REVERT: F 119 GLU cc_start: 0.7555 (tt0) cc_final: 0.7173 (tt0) REVERT: F 142 TYR cc_start: 0.7077 (m-80) cc_final: 0.6174 (m-80) REVERT: G 1430 ASP cc_start: 0.7855 (t70) cc_final: 0.7582 (t0) REVERT: G 1434 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7798 (tm-30) REVERT: G 1555 LYS cc_start: 0.8704 (tttm) cc_final: 0.8216 (tptp) REVERT: H 1420 GLN cc_start: 0.7870 (tm-30) cc_final: 0.7392 (tm-30) REVERT: H 1510 MET cc_start: 0.6349 (mmt) cc_final: 0.4728 (mtm) REVERT: H 1551 THR cc_start: 0.8718 (p) cc_final: 0.8514 (p) REVERT: H 1558 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8199 (mm) REVERT: H 1565 MET cc_start: 0.7683 (tpp) cc_final: 0.6982 (tpp) outliers start: 91 outliers final: 18 residues processed: 688 average time/residue: 0.7433 time to fit residues: 572.7587 Evaluate side-chains 631 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 596 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 802 ARG Chi-restraints excluded: chain A residue 814 ARG Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 829 ARG Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 805 GLN Chi-restraints excluded: chain B residue 829 ARG Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain F residue 39 MET Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 47 PHE Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain G residue 1439 LEU Chi-restraints excluded: chain H residue 1427 VAL Chi-restraints excluded: chain H residue 1455 THR Chi-restraints excluded: chain H residue 1476 THR Chi-restraints excluded: chain H residue 1480 SER Chi-restraints excluded: chain H residue 1548 LEU Chi-restraints excluded: chain H residue 1558 LEU Chi-restraints excluded: chain H residue 1594 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 194 optimal weight: 0.6980 chunk 116 optimal weight: 0.0870 chunk 27 optimal weight: 0.6980 chunk 91 optimal weight: 30.0000 chunk 140 optimal weight: 0.6980 chunk 216 optimal weight: 0.9980 chunk 195 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 chunk 170 optimal weight: 0.2980 chunk 87 optimal weight: 30.0000 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 313 GLN B 189 GLN B 351 ASN B 434 ASN ** B 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 758 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 875 GLN ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN E 94 ASN ** G1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1432 GLN H1434 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.182871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.145537 restraints weight = 47152.654| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.98 r_work: 0.3675 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23896 Z= 0.153 Angle : 0.696 13.189 32089 Z= 0.352 Chirality : 0.041 0.291 3473 Planarity : 0.004 0.094 4217 Dihedral : 6.675 160.944 3151 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.35 % Allowed : 18.36 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.15), residues: 2880 helix: 1.45 (0.12), residues: 1823 sheet: 0.10 (0.36), residues: 194 loop : -0.23 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 802 TYR 0.015 0.001 TYR B 573 PHE 0.039 0.002 PHE D 15 TRP 0.018 0.002 TRP B 828 HIS 0.006 0.001 HIS B 770 Details of bonding type rmsd covalent geometry : bond 0.00346 (23896) covalent geometry : angle 0.69572 (32089) hydrogen bonds : bond 0.04360 ( 1544) hydrogen bonds : angle 4.30371 ( 4506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 606 time to evaluate : 0.746 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: A 136 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7809 (tp30) REVERT: A 161 MET cc_start: 0.8921 (ttp) cc_final: 0.8633 (ttp) REVERT: A 316 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8199 (mptt) REVERT: A 324 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: A 327 ARG cc_start: 0.8031 (ttm-80) cc_final: 0.7790 (ttp80) REVERT: A 400 TYR cc_start: 0.7983 (m-80) cc_final: 0.7756 (m-80) REVERT: A 401 VAL cc_start: 0.8694 (m) cc_final: 0.8296 (t) REVERT: A 544 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7829 (mm-30) REVERT: A 548 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7440 (mp10) REVERT: A 549 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7352 (tm-30) REVERT: A 558 LYS cc_start: 0.8504 (mppt) cc_final: 0.8285 (mppt) REVERT: A 648 GLN cc_start: 0.8132 (mt0) cc_final: 0.7912 (mt0) REVERT: A 662 ARG cc_start: 0.8696 (mtm-85) cc_final: 0.8399 (mtt-85) REVERT: A 752 ASN cc_start: 0.8615 (t0) cc_final: 0.8239 (t0) REVERT: A 802 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8173 (ttm-80) REVERT: A 805 GLN cc_start: 0.8755 (tt0) cc_final: 0.8532 (tt0) REVERT: A 809 MET cc_start: 0.8162 (tpp) cc_final: 0.7932 (tpp) REVERT: A 825 TRP cc_start: 0.7715 (t60) cc_final: 0.7291 (t60) REVERT: A 829 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8104 (pmm-80) REVERT: B 74 LYS cc_start: 0.8325 (mppt) cc_final: 0.8092 (mptt) REVERT: B 146 MET cc_start: 0.8082 (mmp) cc_final: 0.7818 (mmt) REVERT: B 287 HIS cc_start: 0.6971 (t-90) cc_final: 0.6770 (t-170) REVERT: B 324 GLU cc_start: 0.6968 (tm-30) cc_final: 0.6574 (tm-30) REVERT: B 329 MET cc_start: 0.7290 (mmt) cc_final: 0.7040 (tpp) REVERT: B 432 ARG cc_start: 0.7964 (tpt-90) cc_final: 0.7746 (tpt90) REVERT: B 434 ASN cc_start: 0.7130 (m110) cc_final: 0.6914 (m110) REVERT: B 516 GLU cc_start: 0.7183 (pt0) cc_final: 0.6955 (pt0) REVERT: B 517 LYS cc_start: 0.8285 (ttpt) cc_final: 0.7997 (tttp) REVERT: B 540 LYS cc_start: 0.6258 (OUTLIER) cc_final: 0.5796 (tmmm) REVERT: B 583 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7490 (mm-30) REVERT: B 683 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8220 (mp) REVERT: B 774 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7534 (mm-30) REVERT: B 805 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7270 (mm-40) REVERT: B 829 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8137 (ptm-80) REVERT: C 55 LYS cc_start: 0.8426 (mppt) cc_final: 0.8150 (mppt) REVERT: C 70 LEU cc_start: 0.8371 (tm) cc_final: 0.8091 (tt) REVERT: C 73 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7672 (ttm) REVERT: D 15 PHE cc_start: 0.6004 (m-80) cc_final: 0.5647 (m-80) REVERT: D 35 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7251 (tpt) REVERT: D 72 MET cc_start: 0.7679 (tpt) cc_final: 0.7284 (ttp) REVERT: D 119 MET cc_start: 0.6303 (OUTLIER) cc_final: 0.4822 (tpp) REVERT: D 123 GLU cc_start: 0.7699 (mt-10) cc_final: 0.6961 (mt-10) REVERT: E 72 MET cc_start: 0.6477 (ttm) cc_final: 0.6205 (ttm) REVERT: E 97 ASP cc_start: 0.8164 (m-30) cc_final: 0.7406 (m-30) REVERT: E 157 GLU cc_start: 0.7772 (tp30) cc_final: 0.7338 (tp30) REVERT: E 161 ILE cc_start: 0.8262 (mp) cc_final: 0.7935 (mp) REVERT: F 53 LEU cc_start: 0.8785 (tp) cc_final: 0.8223 (tp) REVERT: F 56 MET cc_start: 0.8310 (tmm) cc_final: 0.7968 (mmm) REVERT: F 62 LYS cc_start: 0.5309 (OUTLIER) cc_final: 0.5020 (mmtt) REVERT: F 84 MET cc_start: 0.6099 (ttm) cc_final: 0.5767 (ttm) REVERT: F 88 MET cc_start: 0.6363 (ttt) cc_final: 0.5969 (ttt) REVERT: F 142 TYR cc_start: 0.6914 (m-80) cc_final: 0.6464 (m-80) REVERT: G 1430 ASP cc_start: 0.7851 (t70) cc_final: 0.7602 (t0) REVERT: G 1434 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7838 (tm130) REVERT: G 1515 ASP cc_start: 0.7856 (p0) cc_final: 0.7317 (m-30) REVERT: G 1555 LYS cc_start: 0.8698 (tttm) cc_final: 0.8156 (tptp) REVERT: G 1568 GLN cc_start: 0.8427 (tp40) cc_final: 0.7413 (tp40) REVERT: G 1571 ARG cc_start: 0.8628 (ptp-110) cc_final: 0.8426 (mtm110) REVERT: H 1413 LYS cc_start: 0.8184 (mtmm) cc_final: 0.7817 (pttt) REVERT: H 1420 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7353 (tm-30) REVERT: H 1428 ASP cc_start: 0.7876 (t0) cc_final: 0.7626 (t0) REVERT: H 1444 LYS cc_start: 0.8891 (tmmt) cc_final: 0.7980 (tmmt) REVERT: H 1445 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8293 (tmtm) REVERT: H 1446 PHE cc_start: 0.7983 (m-10) cc_final: 0.7765 (m-80) REVERT: H 1510 MET cc_start: 0.6187 (OUTLIER) cc_final: 0.4799 (mtm) REVERT: H 1558 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8173 (mm) REVERT: H 1565 MET cc_start: 0.7663 (tpp) cc_final: 0.6902 (tpp) outliers start: 85 outliers final: 21 residues processed: 642 average time/residue: 0.7239 time to fit residues: 520.2260 Evaluate side-chains 603 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 566 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 548 GLN Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 802 ARG Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 829 ARG Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain A residue 879 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 689 LEU Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 805 GLN Chi-restraints excluded: chain B residue 829 ARG Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain G residue 1439 LEU Chi-restraints excluded: chain H residue 1445 LYS Chi-restraints excluded: chain H residue 1476 THR Chi-restraints excluded: chain H residue 1510 MET Chi-restraints excluded: chain H residue 1548 LEU Chi-restraints excluded: chain H residue 1558 LEU Chi-restraints excluded: chain H residue 1594 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 76 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 177 optimal weight: 30.0000 chunk 40 optimal weight: 0.4980 chunk 147 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 252 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 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 61 ASN A 68 ASN A 163 GLN ** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 HIS B 189 GLN B 351 ASN B 482 HIS B 500 ASN B 758 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN E 94 ASN F 164 HIS ** G1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1432 GLN ** H1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.182811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.146347 restraints weight = 46797.206| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.91 r_work: 0.3677 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23896 Z= 0.169 Angle : 0.712 15.014 32089 Z= 0.358 Chirality : 0.042 0.302 3473 Planarity : 0.004 0.075 4217 Dihedral : 6.521 168.819 3149 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.86 % Allowed : 18.91 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.15), residues: 2880 helix: 1.56 (0.12), residues: 1815 sheet: 0.17 (0.36), residues: 194 loop : -0.14 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 427 TYR 0.016 0.001 TYR B 300 PHE 0.048 0.002 PHE D 66 TRP 0.020 0.002 TRP B 33 HIS 0.012 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00390 (23896) covalent geometry : angle 0.71249 (32089) hydrogen bonds : bond 0.04323 ( 1544) hydrogen bonds : angle 4.24310 ( 4506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 577 time to evaluate : 0.894 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 94 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7347 (mt-10) REVERT: A 132 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7216 (tp30) REVERT: A 136 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7812 (tp30) REVERT: A 316 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8172 (mptt) REVERT: A 324 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: A 327 ARG cc_start: 0.8041 (ttm-80) cc_final: 0.7763 (ttp80) REVERT: A 355 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8377 (ttmt) REVERT: A 380 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7403 (pt) REVERT: A 400 TYR cc_start: 0.7987 (m-80) cc_final: 0.7768 (m-80) REVERT: A 401 VAL cc_start: 0.8728 (m) cc_final: 0.8368 (t) REVERT: A 498 GLU cc_start: 0.7566 (pp20) cc_final: 0.7298 (pp20) REVERT: A 549 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7355 (tm-30) REVERT: A 558 LYS cc_start: 0.8542 (mppt) cc_final: 0.8308 (mppt) REVERT: A 648 GLN cc_start: 0.8148 (mt0) cc_final: 0.7915 (mt0) REVERT: A 662 ARG cc_start: 0.8704 (mtm-85) cc_final: 0.8420 (mtt-85) REVERT: A 738 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7693 (tp-100) REVERT: A 752 ASN cc_start: 0.8689 (t0) cc_final: 0.8205 (t0) REVERT: A 802 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8188 (ttm-80) REVERT: A 805 GLN cc_start: 0.8798 (tt0) cc_final: 0.8579 (tt0) REVERT: A 809 MET cc_start: 0.8124 (tpp) cc_final: 0.7833 (tpp) REVERT: A 825 TRP cc_start: 0.7711 (t60) cc_final: 0.7353 (t60) REVERT: A 829 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8295 (pmm-80) REVERT: A 875 GLN cc_start: 0.6185 (OUTLIER) cc_final: 0.5913 (mp10) REVERT: B 74 LYS cc_start: 0.8285 (mppt) cc_final: 0.8073 (mptt) REVERT: B 146 MET cc_start: 0.8136 (mmp) cc_final: 0.7855 (mmt) REVERT: B 164 ASP cc_start: 0.8403 (m-30) cc_final: 0.8144 (m-30) REVERT: B 324 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6648 (tm-30) REVERT: B 329 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.7022 (tpp) REVERT: B 423 GLU cc_start: 0.7724 (tt0) cc_final: 0.7122 (tm-30) REVERT: B 434 ASN cc_start: 0.7208 (m110) cc_final: 0.6958 (m110) REVERT: B 516 GLU cc_start: 0.7136 (pt0) cc_final: 0.6858 (pt0) REVERT: B 517 LYS cc_start: 0.8297 (ttpt) cc_final: 0.8016 (tttp) REVERT: B 540 LYS cc_start: 0.6316 (OUTLIER) cc_final: 0.5900 (tmmm) REVERT: B 576 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7809 (ttpt) REVERT: B 611 LEU cc_start: 0.6579 (mt) cc_final: 0.6344 (mp) REVERT: B 683 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8283 (mp) REVERT: B 774 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7458 (mm-30) REVERT: B 804 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: B 829 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8135 (ptm-80) REVERT: C 73 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7760 (ttm) REVERT: C 100 ASN cc_start: 0.7684 (p0) cc_final: 0.7074 (p0) REVERT: D 12 LYS cc_start: 0.8809 (mmmt) cc_final: 0.8600 (mmmt) REVERT: D 35 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7612 (mmm) REVERT: D 72 MET cc_start: 0.7467 (tpt) cc_final: 0.7264 (ttp) REVERT: D 119 MET cc_start: 0.6302 (mmp) cc_final: 0.4903 (tpp) REVERT: D 123 GLU cc_start: 0.7768 (mt-10) cc_final: 0.6934 (mt-10) REVERT: E 72 MET cc_start: 0.6452 (ttm) cc_final: 0.6178 (ttm) REVERT: E 141 LEU cc_start: 0.8812 (mt) cc_final: 0.8596 (mt) REVERT: E 161 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7816 (mp) REVERT: F 56 MET cc_start: 0.8345 (tmm) cc_final: 0.8012 (tmm) REVERT: F 84 MET cc_start: 0.6222 (ttm) cc_final: 0.5883 (ttm) REVERT: F 88 MET cc_start: 0.6379 (ttt) cc_final: 0.5999 (ttt) REVERT: F 119 GLU cc_start: 0.7538 (tt0) cc_final: 0.6528 (tp30) REVERT: F 142 TYR cc_start: 0.7235 (m-80) cc_final: 0.6484 (m-80) REVERT: G 1430 ASP cc_start: 0.7805 (t70) cc_final: 0.7513 (t0) REVERT: G 1434 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7668 (tm130) REVERT: G 1446 PHE cc_start: 0.7231 (t80) cc_final: 0.6835 (t80) REVERT: G 1447 ASP cc_start: 0.7475 (t0) cc_final: 0.7255 (t0) REVERT: G 1555 LYS cc_start: 0.8793 (tttm) cc_final: 0.8196 (tptp) REVERT: G 1568 GLN cc_start: 0.8460 (tp40) cc_final: 0.7542 (tp40) REVERT: G 1571 ARG cc_start: 0.8750 (ptp-110) cc_final: 0.8537 (mtm110) REVERT: H 1410 LYS cc_start: 0.7861 (mtmm) cc_final: 0.7482 (mppt) REVERT: H 1413 LYS cc_start: 0.8237 (mtmm) cc_final: 0.8003 (ptmt) REVERT: H 1420 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7280 (tm-30) REVERT: H 1428 ASP cc_start: 0.7946 (t0) cc_final: 0.7671 (t0) REVERT: H 1442 LYS cc_start: 0.8584 (mttt) cc_final: 0.7974 (mmmt) REVERT: H 1444 LYS cc_start: 0.8649 (tmmt) cc_final: 0.8191 (tmmt) REVERT: H 1445 LYS cc_start: 0.8422 (tmtm) cc_final: 0.8200 (tmtm) REVERT: H 1510 MET cc_start: 0.6080 (OUTLIER) cc_final: 0.4678 (ptt) REVERT: H 1525 LYS cc_start: 0.8115 (mmpt) cc_final: 0.7808 (mtpt) REVERT: H 1558 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8259 (mm) outliers start: 98 outliers final: 29 residues processed: 615 average time/residue: 0.6837 time to fit residues: 471.6357 Evaluate side-chains 597 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 551 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 802 ARG Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 829 ARG Chi-restraints excluded: chain A residue 875 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 805 GLN Chi-restraints excluded: chain B residue 829 ARG Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 47 PHE Chi-restraints excluded: chain G residue 1439 LEU Chi-restraints excluded: chain H residue 1450 LEU Chi-restraints excluded: chain H residue 1510 MET Chi-restraints excluded: chain H residue 1548 LEU Chi-restraints excluded: chain H residue 1558 LEU Chi-restraints excluded: chain H residue 1594 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 246 optimal weight: 2.9990 chunk 177 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 136 optimal weight: 0.3980 chunk 97 optimal weight: 0.6980 chunk 25 optimal weight: 0.0980 chunk 262 optimal weight: 6.9990 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 61 ASN A 68 ASN A 163 GLN A 372 GLN B 189 GLN B 287 HIS B 351 ASN B 758 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN G1563 GLN H1432 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.182338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.145541 restraints weight = 46509.245| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.89 r_work: 0.3665 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23896 Z= 0.162 Angle : 0.712 18.856 32089 Z= 0.355 Chirality : 0.042 0.278 3473 Planarity : 0.004 0.045 4217 Dihedral : 6.451 176.802 3149 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.78 % Allowed : 19.98 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.15), residues: 2880 helix: 1.64 (0.12), residues: 1810 sheet: 0.23 (0.36), residues: 194 loop : -0.16 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 266 TYR 0.020 0.001 TYR A 193 PHE 0.039 0.002 PHE D 15 TRP 0.019 0.001 TRP B 33 HIS 0.011 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00378 (23896) covalent geometry : angle 0.71227 (32089) hydrogen bonds : bond 0.04255 ( 1544) hydrogen bonds : angle 4.21167 ( 4506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 567 time to evaluate : 0.875 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: A 57 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.5856 (pm20) REVERT: A 94 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7407 (mt-10) REVERT: A 136 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7669 (tp30) REVERT: A 248 TYR cc_start: 0.8737 (m-80) cc_final: 0.8126 (m-80) REVERT: A 316 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8165 (mptt) REVERT: A 324 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7702 (tm-30) REVERT: A 327 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7784 (ttp80) REVERT: A 380 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7416 (pt) REVERT: A 400 TYR cc_start: 0.8033 (m-80) cc_final: 0.7830 (m-80) REVERT: A 401 VAL cc_start: 0.8742 (m) cc_final: 0.8395 (t) REVERT: A 498 GLU cc_start: 0.7583 (pp20) cc_final: 0.7326 (pp20) REVERT: A 534 PHE cc_start: 0.4284 (OUTLIER) cc_final: 0.3806 (p90) REVERT: A 549 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7399 (tm-30) REVERT: A 558 LYS cc_start: 0.8537 (mppt) cc_final: 0.8327 (mppt) REVERT: A 648 GLN cc_start: 0.8125 (mt0) cc_final: 0.7910 (mt0) REVERT: A 662 ARG cc_start: 0.8695 (mtm-85) cc_final: 0.8451 (mtt-85) REVERT: A 738 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7724 (tp-100) REVERT: A 752 ASN cc_start: 0.8670 (t0) cc_final: 0.8244 (t0) REVERT: A 802 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8196 (ttm-80) REVERT: A 809 MET cc_start: 0.8132 (tpp) cc_final: 0.7857 (tpp) REVERT: A 825 TRP cc_start: 0.7701 (t60) cc_final: 0.7500 (t60) REVERT: A 829 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8149 (pmm-80) REVERT: B 74 LYS cc_start: 0.8383 (mppt) cc_final: 0.8179 (mptt) REVERT: B 86 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.7269 (mpt) REVERT: B 146 MET cc_start: 0.8135 (mmp) cc_final: 0.7874 (mmt) REVERT: B 164 ASP cc_start: 0.8428 (m-30) cc_final: 0.8151 (m-30) REVERT: B 299 LYS cc_start: 0.6711 (mppt) cc_final: 0.6434 (mtmm) REVERT: B 324 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6662 (tm-30) REVERT: B 423 GLU cc_start: 0.7796 (tt0) cc_final: 0.7175 (tm-30) REVERT: B 434 ASN cc_start: 0.7144 (m-40) cc_final: 0.6876 (m110) REVERT: B 516 GLU cc_start: 0.7114 (pt0) cc_final: 0.6904 (pt0) REVERT: B 517 LYS cc_start: 0.8298 (ttpt) cc_final: 0.8096 (tttp) REVERT: B 540 LYS cc_start: 0.6386 (OUTLIER) cc_final: 0.6002 (tmmm) REVERT: B 576 LYS cc_start: 0.8103 (ttpt) cc_final: 0.7862 (ttpt) REVERT: B 583 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7556 (mm-30) REVERT: B 611 LEU cc_start: 0.6735 (mt) cc_final: 0.6484 (mp) REVERT: B 683 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8127 (mp) REVERT: B 774 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7459 (mm-30) REVERT: B 804 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7478 (tm-30) REVERT: B 829 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8104 (ptm-80) REVERT: C 4 SER cc_start: 0.5477 (OUTLIER) cc_final: 0.4926 (t) REVERT: C 27 LEU cc_start: 0.7745 (mp) cc_final: 0.7107 (mt) REVERT: C 55 LYS cc_start: 0.8449 (mppt) cc_final: 0.8217 (mppt) REVERT: C 73 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7663 (ttm) REVERT: C 125 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7790 (mm-30) REVERT: D 35 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7574 (mmm) REVERT: D 59 MET cc_start: 0.5465 (pp-130) cc_final: 0.5245 (pmm) REVERT: D 119 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.4901 (tpp) REVERT: D 121 GLU cc_start: 0.7896 (pm20) cc_final: 0.7567 (pm20) REVERT: D 122 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7538 (pm20) REVERT: D 123 GLU cc_start: 0.7811 (mt-10) cc_final: 0.6978 (mt-10) REVERT: E 141 LEU cc_start: 0.8778 (mt) cc_final: 0.8572 (mt) REVERT: E 161 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7849 (mp) REVERT: F 53 LEU cc_start: 0.8765 (tp) cc_final: 0.8495 (tp) REVERT: F 56 MET cc_start: 0.8288 (tmm) cc_final: 0.8005 (tmm) REVERT: F 80 ILE cc_start: 0.6498 (pp) cc_final: 0.6285 (pp) REVERT: F 84 MET cc_start: 0.6308 (ttm) cc_final: 0.5911 (ttm) REVERT: F 88 MET cc_start: 0.6414 (ttt) cc_final: 0.5986 (ttt) REVERT: F 89 PHE cc_start: 0.5701 (OUTLIER) cc_final: 0.4886 (t80) REVERT: F 119 GLU cc_start: 0.7504 (tt0) cc_final: 0.6483 (tp30) REVERT: F 142 TYR cc_start: 0.7106 (m-10) cc_final: 0.6358 (m-80) REVERT: G 1430 ASP cc_start: 0.7778 (t70) cc_final: 0.7509 (t0) REVERT: G 1434 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7684 (tm130) REVERT: G 1447 ASP cc_start: 0.7558 (t0) cc_final: 0.7321 (t0) REVERT: G 1464 ARG cc_start: 0.8767 (tmm-80) cc_final: 0.8313 (tmm-80) REVERT: G 1466 ARG cc_start: 0.8434 (mmm-85) cc_final: 0.8053 (mmm-85) REVERT: G 1470 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7209 (mm-30) REVERT: G 1515 ASP cc_start: 0.7807 (p0) cc_final: 0.7315 (m-30) REVERT: G 1555 LYS cc_start: 0.8739 (tttm) cc_final: 0.8170 (tptp) REVERT: G 1571 ARG cc_start: 0.8664 (ptp-110) cc_final: 0.8308 (ptt-90) REVERT: H 1413 LYS cc_start: 0.8222 (mtmm) cc_final: 0.7953 (pttt) REVERT: H 1420 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7267 (tm-30) REVERT: H 1428 ASP cc_start: 0.7948 (t0) cc_final: 0.7671 (t0) REVERT: H 1444 LYS cc_start: 0.8691 (tmmt) cc_final: 0.8286 (tmmt) REVERT: H 1445 LYS cc_start: 0.8440 (tmtm) cc_final: 0.8105 (tmtm) REVERT: H 1510 MET cc_start: 0.6024 (OUTLIER) cc_final: 0.4537 (ptp) REVERT: H 1542 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7380 (mm-30) REVERT: H 1558 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8204 (mm) outliers start: 96 outliers final: 29 residues processed: 606 average time/residue: 0.6932 time to fit residues: 471.4187 Evaluate side-chains 604 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 553 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 677 GLU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 801 LYS Chi-restraints excluded: chain A residue 802 ARG Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 829 ARG Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain B residue 86 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 287 HIS Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 829 ARG Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain F residue 47 PHE Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain H residue 1510 MET Chi-restraints excluded: chain H residue 1556 LEU Chi-restraints excluded: chain H residue 1558 LEU Chi-restraints excluded: chain H residue 1594 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 187 optimal weight: 0.5980 chunk 209 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 236 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 232 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 chunk 244 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 68 ASN A 163 GLN A 372 GLN A 402 GLN B 189 GLN B 287 HIS B 758 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS E 94 ASN F 15 GLN ** G1499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1432 GLN H1434 GLN H1568 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.181626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.144894 restraints weight = 46874.414| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.91 r_work: 0.3650 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23896 Z= 0.180 Angle : 0.740 17.699 32089 Z= 0.368 Chirality : 0.042 0.280 3473 Planarity : 0.004 0.052 4217 Dihedral : 6.397 175.411 3149 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.82 % Allowed : 21.08 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.16), residues: 2880 helix: 1.64 (0.12), residues: 1808 sheet: 0.29 (0.35), residues: 204 loop : -0.22 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 143 TYR 0.018 0.001 TYR A 193 PHE 0.048 0.002 PHE H1446 TRP 0.021 0.002 TRP B 33 HIS 0.022 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00424 (23896) covalent geometry : angle 0.74028 (32089) hydrogen bonds : bond 0.04294 ( 1544) hydrogen bonds : angle 4.25172 ( 4506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 563 time to evaluate : 0.926 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 57 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.5815 (pm20) REVERT: A 136 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7667 (tp30) REVERT: A 248 TYR cc_start: 0.8746 (m-80) cc_final: 0.8138 (m-80) REVERT: A 316 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8184 (mptt) REVERT: A 324 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: A 327 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7745 (ttp80) REVERT: A 355 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8363 (ttmt) REVERT: A 380 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7356 (pt) REVERT: A 400 TYR cc_start: 0.8037 (m-80) cc_final: 0.7819 (m-80) REVERT: A 401 VAL cc_start: 0.8753 (m) cc_final: 0.8425 (t) REVERT: A 498 GLU cc_start: 0.7679 (pp20) cc_final: 0.7407 (pp20) REVERT: A 534 PHE cc_start: 0.4328 (OUTLIER) cc_final: 0.3872 (p90) REVERT: A 549 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7408 (tm-30) REVERT: A 558 LYS cc_start: 0.8582 (mppt) cc_final: 0.8342 (mppt) REVERT: A 648 GLN cc_start: 0.8133 (mt0) cc_final: 0.7897 (mt0) REVERT: A 662 ARG cc_start: 0.8699 (mtm-85) cc_final: 0.8443 (mtt-85) REVERT: A 738 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7700 (tp-100) REVERT: A 802 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8201 (ttm-80) REVERT: A 809 MET cc_start: 0.8151 (tpp) cc_final: 0.7838 (tpp) REVERT: A 829 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8187 (pmm-80) REVERT: B 41 PHE cc_start: 0.3822 (OUTLIER) cc_final: 0.2599 (t80) REVERT: B 74 LYS cc_start: 0.8396 (mppt) cc_final: 0.8166 (mptt) REVERT: B 105 TYR cc_start: 0.6524 (t80) cc_final: 0.6109 (t80) REVERT: B 146 MET cc_start: 0.8192 (mmp) cc_final: 0.7918 (mmt) REVERT: B 164 ASP cc_start: 0.8454 (m-30) cc_final: 0.8250 (m-30) REVERT: B 324 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6726 (tm-30) REVERT: B 329 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.7094 (tpp) REVERT: B 423 GLU cc_start: 0.7815 (tt0) cc_final: 0.7132 (tm-30) REVERT: B 434 ASN cc_start: 0.7189 (m-40) cc_final: 0.6962 (m110) REVERT: B 517 LYS cc_start: 0.8331 (ttpt) cc_final: 0.8085 (tttp) REVERT: B 540 LYS cc_start: 0.6455 (OUTLIER) cc_final: 0.6071 (tmmm) REVERT: B 576 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7798 (ttpt) REVERT: B 583 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7557 (mm-30) REVERT: B 611 LEU cc_start: 0.6684 (mt) cc_final: 0.6435 (mp) REVERT: B 774 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7447 (mm-30) REVERT: B 829 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8099 (ptm-80) REVERT: C 46 GLU cc_start: 0.8665 (tt0) cc_final: 0.8370 (mt-10) REVERT: C 73 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7728 (ttm) REVERT: C 98 GLU cc_start: 0.7778 (pp20) cc_final: 0.7497 (pp20) REVERT: C 125 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7830 (mm-30) REVERT: C 146 MET cc_start: 0.8811 (tmm) cc_final: 0.8522 (ttt) REVERT: D 66 PHE cc_start: 0.4404 (OUTLIER) cc_final: 0.3414 (t80) REVERT: D 119 MET cc_start: 0.6305 (OUTLIER) cc_final: 0.5720 (tpp) REVERT: D 121 GLU cc_start: 0.7980 (pm20) cc_final: 0.7455 (pm20) REVERT: D 122 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7240 (pm20) REVERT: D 123 GLU cc_start: 0.7834 (mt-10) cc_final: 0.6924 (mt-10) REVERT: E 157 GLU cc_start: 0.7752 (tp30) cc_final: 0.7200 (tp30) REVERT: E 161 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7852 (mp) REVERT: F 53 LEU cc_start: 0.8806 (tp) cc_final: 0.8560 (tp) REVERT: F 56 MET cc_start: 0.8308 (tmm) cc_final: 0.8034 (tmm) REVERT: F 80 ILE cc_start: 0.6482 (pp) cc_final: 0.6257 (pp) REVERT: F 84 MET cc_start: 0.6217 (ttm) cc_final: 0.5825 (ttm) REVERT: F 88 MET cc_start: 0.6396 (ttt) cc_final: 0.5969 (ttt) REVERT: F 89 PHE cc_start: 0.5748 (OUTLIER) cc_final: 0.4877 (t80) REVERT: F 119 GLU cc_start: 0.7614 (tt0) cc_final: 0.6772 (tp30) REVERT: F 129 MET cc_start: 0.2939 (OUTLIER) cc_final: 0.1553 (pp-130) REVERT: F 142 TYR cc_start: 0.6999 (m-10) cc_final: 0.6574 (m-80) REVERT: G 1434 GLN cc_start: 0.8102 (tm-30) cc_final: 0.7674 (tm130) REVERT: G 1464 ARG cc_start: 0.8742 (tmm-80) cc_final: 0.8276 (tmm-80) REVERT: G 1494 GLU cc_start: 0.6843 (pp20) cc_final: 0.6566 (pp20) REVERT: G 1506 MET cc_start: 0.2198 (mtt) cc_final: 0.1916 (mtt) REVERT: G 1515 ASP cc_start: 0.7816 (p0) cc_final: 0.7349 (m-30) REVERT: G 1525 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7937 (ttpp) REVERT: G 1555 LYS cc_start: 0.8764 (tttm) cc_final: 0.8248 (tmmt) REVERT: G 1571 ARG cc_start: 0.8677 (ptp-110) cc_final: 0.8461 (mtm110) REVERT: H 1413 LYS cc_start: 0.8232 (mtmm) cc_final: 0.7956 (pttt) REVERT: H 1420 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7248 (tm-30) REVERT: H 1428 ASP cc_start: 0.7944 (t0) cc_final: 0.7679 (t0) REVERT: H 1444 LYS cc_start: 0.8757 (tmmt) cc_final: 0.8288 (ttpp) REVERT: H 1448 GLN cc_start: 0.7973 (mp10) cc_final: 0.7612 (mp10) REVERT: H 1510 MET cc_start: 0.5984 (OUTLIER) cc_final: 0.4591 (ptt) outliers start: 97 outliers final: 30 residues processed: 605 average time/residue: 0.6811 time to fit residues: 462.5880 Evaluate side-chains 598 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 547 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 802 ARG Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 829 ARG Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 287 HIS Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 731 LYS Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 829 ARG Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain F residue 47 PHE Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain G residue 1525 LYS Chi-restraints excluded: chain H residue 1455 THR Chi-restraints excluded: chain H residue 1510 MET Chi-restraints excluded: chain H residue 1534 VAL Chi-restraints excluded: chain H residue 1548 LEU Chi-restraints excluded: chain H residue 1556 LEU Chi-restraints excluded: chain H residue 1594 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 52 optimal weight: 0.6980 chunk 272 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 chunk 198 optimal weight: 0.4980 chunk 89 optimal weight: 9.9990 chunk 170 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 214 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 73 GLN A 163 GLN A 372 GLN A 402 GLN A 752 ASN B 189 GLN B 287 HIS B 758 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 GLN C 41 ASN ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN H1432 GLN H1434 GLN H1568 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.181473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.144795 restraints weight = 46508.006| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.84 r_work: 0.3643 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23896 Z= 0.173 Angle : 0.756 19.000 32089 Z= 0.373 Chirality : 0.042 0.281 3473 Planarity : 0.004 0.054 4217 Dihedral : 6.267 167.288 3149 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.23 % Allowed : 22.50 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.16), residues: 2880 helix: 1.64 (0.12), residues: 1810 sheet: 0.40 (0.36), residues: 200 loop : -0.23 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H1466 TYR 0.021 0.001 TYR A 193 PHE 0.056 0.002 PHE H1446 TRP 0.020 0.001 TRP B 33 HIS 0.023 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00406 (23896) covalent geometry : angle 0.75564 (32089) hydrogen bonds : bond 0.04264 ( 1544) hydrogen bonds : angle 4.25132 ( 4506) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 554 time to evaluate : 0.931 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: A 53 GLU cc_start: 0.8053 (tt0) cc_final: 0.7817 (tt0) REVERT: A 57 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.5801 (pm20) REVERT: A 136 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7527 (tp30) REVERT: A 316 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8192 (mptt) REVERT: A 324 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: A 327 ARG cc_start: 0.8046 (ttm-80) cc_final: 0.7764 (ttp80) REVERT: A 355 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8368 (ttmt) REVERT: A 400 TYR cc_start: 0.8040 (m-80) cc_final: 0.7832 (m-80) REVERT: A 401 VAL cc_start: 0.8787 (m) cc_final: 0.8475 (t) REVERT: A 498 GLU cc_start: 0.7719 (pp20) cc_final: 0.7475 (pp20) REVERT: A 549 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7400 (tm-30) REVERT: A 558 LYS cc_start: 0.8572 (mppt) cc_final: 0.8334 (mppt) REVERT: A 648 GLN cc_start: 0.8119 (mt0) cc_final: 0.7910 (mt0) REVERT: A 662 ARG cc_start: 0.8702 (mtm-85) cc_final: 0.8468 (mtt-85) REVERT: A 738 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7675 (tp-100) REVERT: A 802 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8205 (ttm-80) REVERT: A 809 MET cc_start: 0.8142 (tpp) cc_final: 0.7836 (tpp) REVERT: A 829 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8157 (pmm-80) REVERT: B 41 PHE cc_start: 0.4160 (OUTLIER) cc_final: 0.2899 (t80) REVERT: B 74 LYS cc_start: 0.8392 (mppt) cc_final: 0.8045 (mppt) REVERT: B 105 TYR cc_start: 0.6788 (t80) cc_final: 0.6221 (t80) REVERT: B 109 LEU cc_start: 0.7766 (mt) cc_final: 0.7560 (mm) REVERT: B 146 MET cc_start: 0.8177 (mmp) cc_final: 0.7928 (mmt) REVERT: B 161 MET cc_start: 0.8598 (ttp) cc_final: 0.8387 (ttm) REVERT: B 324 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6742 (tm-30) REVERT: B 423 GLU cc_start: 0.7796 (tt0) cc_final: 0.7204 (tm-30) REVERT: B 434 ASN cc_start: 0.7178 (m-40) cc_final: 0.6972 (m110) REVERT: B 517 LYS cc_start: 0.8338 (ttpt) cc_final: 0.8131 (tttp) REVERT: B 540 LYS cc_start: 0.6590 (OUTLIER) cc_final: 0.6204 (tmmm) REVERT: B 576 LYS cc_start: 0.8059 (ttpt) cc_final: 0.7772 (ttpt) REVERT: B 583 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7594 (mm-30) REVERT: B 611 LEU cc_start: 0.6717 (mt) cc_final: 0.6468 (mp) REVERT: B 774 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7500 (mm-30) REVERT: B 829 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8010 (ptm-80) REVERT: C 73 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7664 (ttm) REVERT: C 125 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7788 (mm-30) REVERT: C 146 MET cc_start: 0.8722 (tmm) cc_final: 0.8385 (ttt) REVERT: D 66 PHE cc_start: 0.4260 (OUTLIER) cc_final: 0.3250 (t80) REVERT: D 119 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.5803 (tpp) REVERT: D 123 GLU cc_start: 0.7847 (mt-10) cc_final: 0.6988 (mt-10) REVERT: E 157 GLU cc_start: 0.7706 (tp30) cc_final: 0.7151 (tp30) REVERT: E 161 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7872 (mp) REVERT: F 53 LEU cc_start: 0.8776 (tp) cc_final: 0.8534 (tp) REVERT: F 56 MET cc_start: 0.8257 (tmm) cc_final: 0.7994 (tmm) REVERT: F 80 ILE cc_start: 0.6697 (pp) cc_final: 0.6477 (pp) REVERT: F 84 MET cc_start: 0.6262 (ttm) cc_final: 0.5896 (ttm) REVERT: F 88 MET cc_start: 0.6438 (ttt) cc_final: 0.6025 (ttt) REVERT: F 89 PHE cc_start: 0.5787 (OUTLIER) cc_final: 0.4906 (t80) REVERT: F 119 GLU cc_start: 0.7438 (tt0) cc_final: 0.6636 (tp30) REVERT: F 129 MET cc_start: 0.2805 (OUTLIER) cc_final: 0.1264 (pp-130) REVERT: F 142 TYR cc_start: 0.7112 (m-10) cc_final: 0.6503 (m-80) REVERT: G 1434 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7712 (tm130) REVERT: G 1464 ARG cc_start: 0.8698 (tmm-80) cc_final: 0.8212 (tmm-80) REVERT: G 1494 GLU cc_start: 0.6789 (pp20) cc_final: 0.6555 (pp20) REVERT: G 1515 ASP cc_start: 0.7721 (p0) cc_final: 0.7322 (m-30) REVERT: G 1525 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7972 (ttpp) REVERT: G 1555 LYS cc_start: 0.8754 (tttm) cc_final: 0.8117 (tptp) REVERT: H 1413 LYS cc_start: 0.8242 (mtmm) cc_final: 0.7939 (pttt) REVERT: H 1420 GLN cc_start: 0.7894 (tm-30) cc_final: 0.7223 (tm-30) REVERT: H 1428 ASP cc_start: 0.8015 (t0) cc_final: 0.7736 (t0) REVERT: H 1444 LYS cc_start: 0.8738 (tmmt) cc_final: 0.8157 (ttpp) REVERT: H 1448 GLN cc_start: 0.7931 (mp10) cc_final: 0.7571 (mp10) REVERT: H 1459 LYS cc_start: 0.8730 (mmmm) cc_final: 0.7935 (ttpp) REVERT: H 1510 MET cc_start: 0.5728 (OUTLIER) cc_final: 0.4322 (ptt) REVERT: H 1557 ARG cc_start: 0.8724 (mtt180) cc_final: 0.8330 (mtt180) REVERT: H 1558 LEU cc_start: 0.8552 (mm) cc_final: 0.8335 (mm) outliers start: 82 outliers final: 34 residues processed: 591 average time/residue: 0.7010 time to fit residues: 463.5120 Evaluate side-chains 593 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 541 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 802 ARG Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 829 ARG Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 287 HIS Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 731 LYS Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 829 ARG Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain G residue 1525 LYS Chi-restraints excluded: chain H residue 1445 LYS Chi-restraints excluded: chain H residue 1455 THR Chi-restraints excluded: chain H residue 1510 MET Chi-restraints excluded: chain H residue 1534 VAL Chi-restraints excluded: chain H residue 1548 LEU Chi-restraints excluded: chain H residue 1556 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 264 optimal weight: 6.9990 chunk 238 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 174 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 282 optimal weight: 10.0000 chunk 271 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 246 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 68 ASN A 163 GLN A 372 GLN A 402 GLN B 189 GLN B 287 HIS B 351 ASN B 758 GLN ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN H1432 GLN H1434 GLN H1568 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.181610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.145105 restraints weight = 46635.609| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.85 r_work: 0.3653 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23896 Z= 0.180 Angle : 0.788 18.646 32089 Z= 0.389 Chirality : 0.043 0.274 3473 Planarity : 0.004 0.054 4217 Dihedral : 6.185 160.566 3149 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.84 % Allowed : 23.84 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.16), residues: 2880 helix: 1.58 (0.12), residues: 1817 sheet: 0.46 (0.36), residues: 198 loop : -0.35 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G1571 TYR 0.031 0.001 TYR A 193 PHE 0.034 0.002 PHE D 15 TRP 0.019 0.001 TRP B 33 HIS 0.019 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00426 (23896) covalent geometry : angle 0.78781 (32089) hydrogen bonds : bond 0.04293 ( 1544) hydrogen bonds : angle 4.29958 ( 4506) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 555 time to evaluate : 0.930 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: A 53 GLU cc_start: 0.7987 (tt0) cc_final: 0.7727 (tt0) REVERT: A 57 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.5798 (pm20) REVERT: A 132 GLU cc_start: 0.7507 (tp30) cc_final: 0.6954 (tm-30) REVERT: A 136 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7744 (tp30) REVERT: A 316 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8168 (mptt) REVERT: A 324 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: A 327 ARG cc_start: 0.8052 (ttm-80) cc_final: 0.7773 (ttp80) REVERT: A 355 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8373 (ttmt) REVERT: A 400 TYR cc_start: 0.8013 (m-80) cc_final: 0.7779 (m-80) REVERT: A 401 VAL cc_start: 0.8792 (m) cc_final: 0.8389 (t) REVERT: A 402 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8242 (mp-120) REVERT: A 498 GLU cc_start: 0.7737 (pp20) cc_final: 0.7494 (pp20) REVERT: A 549 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7408 (tm-30) REVERT: A 558 LYS cc_start: 0.8568 (mppt) cc_final: 0.8279 (mppt) REVERT: A 648 GLN cc_start: 0.8122 (mt0) cc_final: 0.7909 (mt0) REVERT: A 662 ARG cc_start: 0.8693 (mtm-85) cc_final: 0.8450 (mtt-85) REVERT: A 738 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7683 (tp-100) REVERT: A 802 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8186 (ttm-80) REVERT: A 809 MET cc_start: 0.8133 (tpp) cc_final: 0.7830 (tpp) REVERT: A 829 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8192 (pmm-80) REVERT: B 41 PHE cc_start: 0.4310 (OUTLIER) cc_final: 0.2908 (t80) REVERT: B 74 LYS cc_start: 0.8396 (mppt) cc_final: 0.8045 (mppt) REVERT: B 105 TYR cc_start: 0.7062 (t80) cc_final: 0.6466 (t80) REVERT: B 109 LEU cc_start: 0.7764 (mt) cc_final: 0.7542 (mm) REVERT: B 146 MET cc_start: 0.8232 (mmp) cc_final: 0.7966 (mmt) REVERT: B 161 MET cc_start: 0.8601 (ttp) cc_final: 0.8392 (ttm) REVERT: B 320 GLN cc_start: 0.6916 (pp30) cc_final: 0.6649 (pm20) REVERT: B 324 GLU cc_start: 0.7338 (tm-30) cc_final: 0.6795 (tm-30) REVERT: B 372 GLN cc_start: 0.7757 (pt0) cc_final: 0.7483 (pp30) REVERT: B 423 GLU cc_start: 0.7797 (tt0) cc_final: 0.7168 (tm-30) REVERT: B 434 ASN cc_start: 0.7135 (m-40) cc_final: 0.6910 (m110) REVERT: B 540 LYS cc_start: 0.6630 (OUTLIER) cc_final: 0.6230 (tmmm) REVERT: B 576 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7755 (ttpt) REVERT: B 583 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7590 (mm-30) REVERT: B 611 LEU cc_start: 0.6655 (mt) cc_final: 0.6403 (mp) REVERT: B 774 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7483 (mm-30) REVERT: B 829 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8024 (ptm-80) REVERT: C 73 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7691 (ttm) REVERT: C 125 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7796 (mm-30) REVERT: C 146 MET cc_start: 0.8703 (tmm) cc_final: 0.8337 (ttt) REVERT: D 66 PHE cc_start: 0.4306 (OUTLIER) cc_final: 0.3886 (t80) REVERT: D 119 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.5962 (tpp) REVERT: D 122 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7198 (pm20) REVERT: D 123 GLU cc_start: 0.7811 (mt-10) cc_final: 0.6937 (mt-10) REVERT: E 39 MET cc_start: 0.7487 (tmt) cc_final: 0.7278 (tmm) REVERT: E 157 GLU cc_start: 0.7723 (tp30) cc_final: 0.7166 (tp30) REVERT: E 161 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7868 (mp) REVERT: F 53 LEU cc_start: 0.8777 (tp) cc_final: 0.8540 (tp) REVERT: F 56 MET cc_start: 0.8259 (tmm) cc_final: 0.8003 (tmm) REVERT: F 80 ILE cc_start: 0.6735 (pp) cc_final: 0.6461 (pp) REVERT: F 84 MET cc_start: 0.6281 (ttm) cc_final: 0.5905 (ttm) REVERT: F 88 MET cc_start: 0.6437 (ttt) cc_final: 0.6015 (ttt) REVERT: F 89 PHE cc_start: 0.5791 (OUTLIER) cc_final: 0.4899 (t80) REVERT: F 119 GLU cc_start: 0.7549 (tt0) cc_final: 0.6769 (tp30) REVERT: F 129 MET cc_start: 0.3055 (OUTLIER) cc_final: 0.1485 (pp-130) REVERT: F 142 TYR cc_start: 0.7170 (m-10) cc_final: 0.6562 (m-80) REVERT: G 1434 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7718 (tm130) REVERT: G 1444 LYS cc_start: 0.7872 (mmpt) cc_final: 0.7589 (mmmm) REVERT: G 1464 ARG cc_start: 0.8671 (tmm-80) cc_final: 0.8170 (tmm-80) REVERT: G 1494 GLU cc_start: 0.6900 (pp20) cc_final: 0.6654 (pp20) REVERT: G 1506 MET cc_start: 0.2136 (mtt) cc_final: 0.1447 (mtt) REVERT: G 1515 ASP cc_start: 0.7776 (p0) cc_final: 0.7349 (m-30) REVERT: G 1525 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7984 (ttpp) REVERT: G 1555 LYS cc_start: 0.8753 (tttm) cc_final: 0.8147 (tptp) REVERT: H 1413 LYS cc_start: 0.8252 (mtmm) cc_final: 0.7968 (pttt) REVERT: H 1420 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7220 (tm-30) REVERT: H 1428 ASP cc_start: 0.7975 (t0) cc_final: 0.7704 (t0) REVERT: H 1444 LYS cc_start: 0.8742 (tmmt) cc_final: 0.7966 (tmmt) REVERT: H 1448 GLN cc_start: 0.7997 (mp10) cc_final: 0.7702 (mp10) REVERT: H 1459 LYS cc_start: 0.8738 (mmmm) cc_final: 0.7914 (ttpp) REVERT: H 1510 MET cc_start: 0.5820 (OUTLIER) cc_final: 0.4452 (ptp) outliers start: 72 outliers final: 32 residues processed: 587 average time/residue: 0.7619 time to fit residues: 499.5668 Evaluate side-chains 587 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 535 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 355 LYS Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 801 LYS Chi-restraints excluded: chain A residue 802 ARG Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 829 ARG Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 287 HIS Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 731 LYS Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 829 ARG Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain G residue 1450 LEU Chi-restraints excluded: chain G residue 1525 LYS Chi-restraints excluded: chain H residue 1510 MET Chi-restraints excluded: chain H residue 1534 VAL Chi-restraints excluded: chain H residue 1548 LEU Chi-restraints excluded: chain H residue 1556 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 227 optimal weight: 3.9990 chunk 130 optimal weight: 0.0570 chunk 89 optimal weight: 0.0970 chunk 72 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 253 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 234 optimal weight: 0.6980 chunk 92 optimal weight: 0.0040 chunk 40 optimal weight: 0.9990 overall best weight: 0.2708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 163 GLN A 372 GLN A 752 ASN B 189 GLN B 287 HIS B 758 GLN ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN G1579 GLN H1540 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.180695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.144418 restraints weight = 47082.256| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.99 r_work: 0.3659 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23896 Z= 0.148 Angle : 0.808 19.795 32089 Z= 0.396 Chirality : 0.042 0.290 3473 Planarity : 0.004 0.062 4217 Dihedral : 6.065 157.219 3149 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.60 % Allowed : 24.39 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.16), residues: 2880 helix: 1.74 (0.12), residues: 1813 sheet: 0.62 (0.37), residues: 198 loop : -0.37 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G1571 TYR 0.026 0.001 TYR A 193 PHE 0.036 0.002 PHE D 15 TRP 0.017 0.001 TRP B 828 HIS 0.013 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00341 (23896) covalent geometry : angle 0.80847 (32089) hydrogen bonds : bond 0.04177 ( 1544) hydrogen bonds : angle 4.27005 ( 4506) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 559 time to evaluate : 0.923 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: A 53 GLU cc_start: 0.7948 (tt0) cc_final: 0.7711 (tt0) REVERT: A 57 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.5795 (pm20) REVERT: A 132 GLU cc_start: 0.7500 (tp30) cc_final: 0.7235 (tm-30) REVERT: A 136 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7831 (tp30) REVERT: A 142 LYS cc_start: 0.8689 (mppt) cc_final: 0.8300 (mppt) REVERT: A 248 TYR cc_start: 0.8719 (m-80) cc_final: 0.8120 (m-80) REVERT: A 316 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8169 (mptt) REVERT: A 324 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: A 327 ARG cc_start: 0.8035 (ttm-80) cc_final: 0.7738 (ttp80) REVERT: A 361 ASP cc_start: 0.7093 (t0) cc_final: 0.6820 (t70) REVERT: A 498 GLU cc_start: 0.7752 (pp20) cc_final: 0.7503 (pp20) REVERT: A 549 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7411 (tm-30) REVERT: A 558 LYS cc_start: 0.8554 (mppt) cc_final: 0.8244 (mppt) REVERT: A 648 GLN cc_start: 0.8132 (mt0) cc_final: 0.7915 (mt0) REVERT: A 662 ARG cc_start: 0.8707 (mtm-85) cc_final: 0.8471 (mtt-85) REVERT: A 738 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7666 (tp-100) REVERT: A 802 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8197 (ttm-80) REVERT: A 809 MET cc_start: 0.8161 (tpp) cc_final: 0.7855 (tpp) REVERT: A 829 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8180 (pmm-80) REVERT: B 41 PHE cc_start: 0.4267 (OUTLIER) cc_final: 0.3018 (t80) REVERT: B 74 LYS cc_start: 0.8372 (mppt) cc_final: 0.7994 (mppt) REVERT: B 105 TYR cc_start: 0.7070 (t80) cc_final: 0.6399 (t80) REVERT: B 146 MET cc_start: 0.8232 (mmp) cc_final: 0.7961 (mmt) REVERT: B 161 MET cc_start: 0.8612 (ttp) cc_final: 0.8398 (ttm) REVERT: B 320 GLN cc_start: 0.6920 (pp30) cc_final: 0.6660 (pm20) REVERT: B 324 GLU cc_start: 0.7325 (tm-30) cc_final: 0.6762 (tm-30) REVERT: B 372 GLN cc_start: 0.7756 (pt0) cc_final: 0.7474 (pp30) REVERT: B 432 ARG cc_start: 0.8069 (tpt90) cc_final: 0.7830 (ttt90) REVERT: B 434 ASN cc_start: 0.7132 (m-40) cc_final: 0.6914 (m110) REVERT: B 540 LYS cc_start: 0.6608 (OUTLIER) cc_final: 0.6213 (tmmm) REVERT: B 576 LYS cc_start: 0.8102 (ttpt) cc_final: 0.7755 (ttpt) REVERT: B 583 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7626 (mm-30) REVERT: B 611 LEU cc_start: 0.6620 (mt) cc_final: 0.6365 (mp) REVERT: B 774 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7512 (mm-30) REVERT: B 829 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8049 (ptm-80) REVERT: C 73 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7645 (ttm) REVERT: C 125 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7854 (mm-30) REVERT: C 146 MET cc_start: 0.8681 (tmm) cc_final: 0.8453 (ttt) REVERT: D 66 PHE cc_start: 0.3966 (OUTLIER) cc_final: 0.3547 (t80) REVERT: D 119 MET cc_start: 0.6875 (OUTLIER) cc_final: 0.5893 (tpp) REVERT: D 121 GLU cc_start: 0.7701 (pm20) cc_final: 0.6796 (pm20) REVERT: D 122 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7075 (pm20) REVERT: D 123 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7065 (mt-10) REVERT: E 31 GLN cc_start: 0.7835 (pp30) cc_final: 0.7377 (pp30) REVERT: E 39 MET cc_start: 0.7489 (tmt) cc_final: 0.7283 (tmm) REVERT: E 157 GLU cc_start: 0.7732 (tp30) cc_final: 0.7170 (tp30) REVERT: E 161 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7844 (mp) REVERT: F 53 LEU cc_start: 0.8808 (tp) cc_final: 0.8570 (tp) REVERT: F 56 MET cc_start: 0.8280 (tmm) cc_final: 0.8007 (tmm) REVERT: F 80 ILE cc_start: 0.6775 (pp) cc_final: 0.6476 (pp) REVERT: F 84 MET cc_start: 0.6274 (ttm) cc_final: 0.5890 (ttm) REVERT: F 88 MET cc_start: 0.6392 (ttt) cc_final: 0.5925 (ttt) REVERT: F 89 PHE cc_start: 0.5715 (OUTLIER) cc_final: 0.4860 (t80) REVERT: F 119 GLU cc_start: 0.7588 (tt0) cc_final: 0.6826 (tp30) REVERT: F 142 TYR cc_start: 0.7173 (m-10) cc_final: 0.6591 (m-80) REVERT: G 1434 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7701 (tm130) REVERT: G 1444 LYS cc_start: 0.7890 (mmpt) cc_final: 0.7672 (mmmm) REVERT: G 1459 LYS cc_start: 0.8987 (mmpt) cc_final: 0.8612 (mttt) REVERT: G 1464 ARG cc_start: 0.8668 (tmm-80) cc_final: 0.8161 (tmm-80) REVERT: G 1494 GLU cc_start: 0.6995 (pp20) cc_final: 0.6749 (pp20) REVERT: G 1515 ASP cc_start: 0.7836 (p0) cc_final: 0.7432 (m-30) REVERT: G 1525 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7956 (ttpp) REVERT: G 1555 LYS cc_start: 0.8758 (tttm) cc_final: 0.8131 (tptp) REVERT: G 1607 MET cc_start: 0.6655 (tmm) cc_final: 0.6040 (ptp) REVERT: H 1413 LYS cc_start: 0.8254 (mtmm) cc_final: 0.7956 (pttt) REVERT: H 1420 GLN cc_start: 0.7868 (tm-30) cc_final: 0.7204 (tm-30) REVERT: H 1428 ASP cc_start: 0.7968 (t0) cc_final: 0.7689 (t0) REVERT: H 1444 LYS cc_start: 0.8730 (tmmt) cc_final: 0.7982 (tmmt) REVERT: H 1448 GLN cc_start: 0.8061 (mp10) cc_final: 0.7690 (mp10) REVERT: H 1459 LYS cc_start: 0.8733 (mmmm) cc_final: 0.7940 (ttpp) REVERT: H 1489 MET cc_start: 0.6571 (pp-130) cc_final: 0.6224 (ppp) REVERT: H 1510 MET cc_start: 0.5701 (OUTLIER) cc_final: 0.4283 (ptt) REVERT: H 1532 GLN cc_start: 0.8317 (tm-30) cc_final: 0.7967 (tm130) REVERT: H 1557 ARG cc_start: 0.8635 (mtt180) cc_final: 0.8410 (mtt180) REVERT: H 1565 MET cc_start: 0.8021 (tpp) cc_final: 0.7532 (tpp) outliers start: 66 outliers final: 27 residues processed: 586 average time/residue: 0.7788 time to fit residues: 509.1247 Evaluate side-chains 581 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 537 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 802 ARG Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 829 ARG Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 257 TYR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 731 LYS Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 829 ARG Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain G residue 1525 LYS Chi-restraints excluded: chain H residue 1445 LYS Chi-restraints excluded: chain H residue 1510 MET Chi-restraints excluded: chain H residue 1534 VAL Chi-restraints excluded: chain H residue 1556 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 72 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 233 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 270 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 254 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 163 GLN A 372 GLN B 122 ASN B 189 GLN B 758 GLN B 770 HIS ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN G1501 GLN H1432 GLN H1434 GLN H1568 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.181207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.144900 restraints weight = 46893.093| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 3.03 r_work: 0.3615 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 23896 Z= 0.198 Angle : 0.855 18.044 32089 Z= 0.420 Chirality : 0.046 0.463 3473 Planarity : 0.005 0.101 4217 Dihedral : 6.068 151.987 3149 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.17 % Allowed : 25.10 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.16), residues: 2880 helix: 1.67 (0.12), residues: 1813 sheet: 0.48 (0.36), residues: 198 loop : -0.45 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 427 TYR 0.026 0.002 TYR A 193 PHE 0.033 0.002 PHE D 15 TRP 0.019 0.002 TRP B 828 HIS 0.010 0.001 HIS B 770 Details of bonding type rmsd covalent geometry : bond 0.00473 (23896) covalent geometry : angle 0.85530 (32089) hydrogen bonds : bond 0.04344 ( 1544) hydrogen bonds : angle 4.34323 ( 4506) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 553 time to evaluate : 0.888 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 53 GLU cc_start: 0.8007 (tt0) cc_final: 0.7792 (tt0) REVERT: A 132 GLU cc_start: 0.7540 (tp30) cc_final: 0.6986 (tm-30) REVERT: A 136 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7788 (tp30) REVERT: A 248 TYR cc_start: 0.8786 (m-80) cc_final: 0.8231 (m-80) REVERT: A 316 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8201 (mptt) REVERT: A 324 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: A 327 ARG cc_start: 0.8073 (ttm-80) cc_final: 0.7767 (ttp80) REVERT: A 361 ASP cc_start: 0.7135 (t0) cc_final: 0.6689 (t0) REVERT: A 401 VAL cc_start: 0.8859 (m) cc_final: 0.8484 (t) REVERT: A 498 GLU cc_start: 0.7789 (pp20) cc_final: 0.7549 (pp20) REVERT: A 549 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7413 (tm-30) REVERT: A 558 LYS cc_start: 0.8579 (mppt) cc_final: 0.8292 (mppt) REVERT: A 648 GLN cc_start: 0.8159 (mt0) cc_final: 0.7956 (mt0) REVERT: A 662 ARG cc_start: 0.8719 (mtm-85) cc_final: 0.8476 (mtt-85) REVERT: A 738 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7737 (tp-100) REVERT: A 809 MET cc_start: 0.8178 (tpp) cc_final: 0.7850 (tpp) REVERT: A 829 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8179 (pmm-80) REVERT: B 41 PHE cc_start: 0.4499 (OUTLIER) cc_final: 0.4203 (t80) REVERT: B 74 LYS cc_start: 0.8339 (mppt) cc_final: 0.7939 (mppt) REVERT: B 75 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.6880 (mtp) REVERT: B 105 TYR cc_start: 0.7218 (t80) cc_final: 0.6486 (t80) REVERT: B 146 MET cc_start: 0.8263 (mmp) cc_final: 0.7998 (mmt) REVERT: B 161 MET cc_start: 0.8650 (ttp) cc_final: 0.8443 (ttm) REVERT: B 320 GLN cc_start: 0.6939 (pp30) cc_final: 0.6687 (pm20) REVERT: B 323 MET cc_start: 0.6840 (mmm) cc_final: 0.6480 (mmm) REVERT: B 324 GLU cc_start: 0.7437 (tm-30) cc_final: 0.6882 (tm-30) REVERT: B 329 MET cc_start: 0.7348 (mmp) cc_final: 0.7142 (mmm) REVERT: B 372 GLN cc_start: 0.7779 (pt0) cc_final: 0.7489 (pp30) REVERT: B 423 GLU cc_start: 0.7795 (tt0) cc_final: 0.7179 (tm-30) REVERT: B 434 ASN cc_start: 0.7151 (m-40) cc_final: 0.6889 (m110) REVERT: B 540 LYS cc_start: 0.6574 (OUTLIER) cc_final: 0.6157 (tmmm) REVERT: B 576 LYS cc_start: 0.8118 (ttpt) cc_final: 0.7797 (ttpt) REVERT: B 583 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7669 (mm-30) REVERT: B 611 LEU cc_start: 0.6698 (mt) cc_final: 0.6433 (mp) REVERT: B 774 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7539 (mm-30) REVERT: B 829 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8092 (ptm-80) REVERT: C 73 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7796 (ttm) REVERT: C 93 ARG cc_start: 0.8545 (ttm-80) cc_final: 0.8337 (tpp80) REVERT: C 125 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7871 (mm-30) REVERT: D 66 PHE cc_start: 0.4087 (OUTLIER) cc_final: 0.3693 (t80) REVERT: D 119 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.5804 (tpp) REVERT: D 121 GLU cc_start: 0.7841 (pm20) cc_final: 0.7010 (pm20) REVERT: D 122 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7183 (pm20) REVERT: D 123 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7103 (mt-10) REVERT: E 31 GLN cc_start: 0.7866 (pp30) cc_final: 0.7482 (pp30) REVERT: E 157 GLU cc_start: 0.7735 (tp30) cc_final: 0.7200 (tp30) REVERT: E 161 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7908 (mp) REVERT: F 53 LEU cc_start: 0.8826 (tp) cc_final: 0.8596 (tp) REVERT: F 56 MET cc_start: 0.8309 (tmm) cc_final: 0.8053 (tmm) REVERT: F 80 ILE cc_start: 0.6797 (pp) cc_final: 0.6507 (pp) REVERT: F 84 MET cc_start: 0.6322 (ttm) cc_final: 0.5962 (ttm) REVERT: F 88 MET cc_start: 0.6444 (ttt) cc_final: 0.6015 (ttt) REVERT: F 89 PHE cc_start: 0.5765 (OUTLIER) cc_final: 0.4849 (t80) REVERT: F 119 GLU cc_start: 0.7413 (tt0) cc_final: 0.6627 (tp30) REVERT: F 142 TYR cc_start: 0.7175 (m-10) cc_final: 0.6595 (m-80) REVERT: G 1434 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7715 (tm130) REVERT: G 1444 LYS cc_start: 0.7949 (mmpt) cc_final: 0.7721 (mmmm) REVERT: G 1459 LYS cc_start: 0.8969 (mmpt) cc_final: 0.8752 (mmtm) REVERT: G 1494 GLU cc_start: 0.6908 (pp20) cc_final: 0.6698 (pp20) REVERT: G 1506 MET cc_start: 0.2228 (mtt) cc_final: 0.1792 (mtt) REVERT: G 1515 ASP cc_start: 0.7764 (p0) cc_final: 0.7369 (m-30) REVERT: G 1555 LYS cc_start: 0.8783 (tttm) cc_final: 0.8228 (tptp) REVERT: G 1557 ARG cc_start: 0.7531 (tmm-80) cc_final: 0.6928 (tmm-80) REVERT: G 1568 GLN cc_start: 0.8676 (tp40) cc_final: 0.8238 (tp40) REVERT: G 1607 MET cc_start: 0.6750 (tmm) cc_final: 0.6295 (ptt) REVERT: H 1413 LYS cc_start: 0.8282 (mtmm) cc_final: 0.7958 (pttt) REVERT: H 1420 GLN cc_start: 0.7865 (tm-30) cc_final: 0.7191 (tm-30) REVERT: H 1428 ASP cc_start: 0.8008 (t0) cc_final: 0.7731 (t0) REVERT: H 1444 LYS cc_start: 0.8758 (tmmt) cc_final: 0.8017 (tmmt) REVERT: H 1448 GLN cc_start: 0.8033 (mp10) cc_final: 0.7655 (mp10) REVERT: H 1459 LYS cc_start: 0.8757 (mmmm) cc_final: 0.7922 (ttpp) REVERT: H 1489 MET cc_start: 0.6458 (pp-130) cc_final: 0.6131 (ppp) REVERT: H 1510 MET cc_start: 0.5708 (OUTLIER) cc_final: 0.4254 (ptt) REVERT: H 1565 MET cc_start: 0.8097 (tpp) cc_final: 0.7628 (tpp) outliers start: 55 outliers final: 26 residues processed: 574 average time/residue: 0.7966 time to fit residues: 510.5700 Evaluate side-chains 576 residues out of total 2538 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 535 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 805 GLN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 829 ARG Chi-restraints excluded: chain A residue 841 SER Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 731 LYS Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 780 THR Chi-restraints excluded: chain B residue 829 ARG Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 66 ASP Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain H residue 1510 MET Chi-restraints excluded: chain H residue 1534 VAL Chi-restraints excluded: chain H residue 1556 LEU Chi-restraints excluded: chain H residue 1558 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 169 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 260 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 chunk 280 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 206 optimal weight: 0.0170 chunk 277 optimal weight: 0.9990 chunk 264 optimal weight: 7.9990 chunk 182 optimal weight: 0.5980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 372 GLN A 752 ASN B 189 GLN B 758 GLN B 770 HIS ** B 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN G1501 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.181272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.144824 restraints weight = 46703.731| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.88 r_work: 0.3643 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 23896 Z= 0.182 Angle : 0.863 17.245 32089 Z= 0.423 Chirality : 0.045 0.481 3473 Planarity : 0.005 0.094 4217 Dihedral : 6.057 149.966 3149 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.29 % Allowed : 25.14 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.16), residues: 2880 helix: 1.61 (0.12), residues: 1820 sheet: 0.51 (0.37), residues: 196 loop : -0.51 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 427 TYR 0.025 0.002 TYR A 193 PHE 0.050 0.002 PHE H1446 TRP 0.018 0.001 TRP B 828 HIS 0.010 0.001 HIS B 770 Details of bonding type rmsd covalent geometry : bond 0.00431 (23896) covalent geometry : angle 0.86275 (32089) hydrogen bonds : bond 0.04368 ( 1544) hydrogen bonds : angle 4.37687 ( 4506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10716.36 seconds wall clock time: 182 minutes 48.37 seconds (10968.37 seconds total)