Starting phenix.real_space_refine on Wed Nov 20 03:03:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7q_18229/11_2024/8q7q_18229_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7q_18229/11_2024/8q7q_18229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7q_18229/11_2024/8q7q_18229.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7q_18229/11_2024/8q7q_18229.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7q_18229/11_2024/8q7q_18229_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7q_18229/11_2024/8q7q_18229_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.044 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: 7 Type Number sf(0) Gaussians P 106 5.49 5 Mg 1 5.21 5 S 109 5.16 5 C 17705 2.51 5 N 5061 2.21 5 O 5598 1.98 5 H 25117 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 179 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 53697 Number of models: 1 Model: "" Number of chains: 16 Chain: "5" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 3301 Classifications: {'RNA': 104} Modifications used: {'3*END': 1, '5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 15, 'rna3p_pur': 39, 'rna3p_pyr': 42} Link IDs: {'rna2p': 22, 'rna3p': 81} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 27194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1645, 27194 Classifications: {'peptide': 1645} Link IDs: {'PCIS': 3, 'PTRANS': 90, 'TRANS': 1551} Chain breaks: 8 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 2, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 432 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "C" Number of atoms: 13374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 846, 13374 Classifications: {'peptide': 846} Link IDs: {'PTRANS': 49, 'TRANS': 796} Chain: "D" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2193 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 295} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 936 Unresolved non-hydrogen angles: 1208 Unresolved non-hydrogen dihedrals: 796 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 16, 'GLN%COO:plan1': 1, 'TYR:plan': 11, 'ASN:plan1': 15, 'TRP:plan': 7, 'HIS:plan': 9, 'PHE:plan': 11, 'GLU:plan': 11, 'ASP:plan': 22} Unresolved non-hydrogen planarities: 522 Chain: "F" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 173 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "G" Number of atoms: 1983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain breaks: 2 Chain: "H" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 357 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Chain: "a" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "b" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 511 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 125 Chain: "c" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 688 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 165 Chain: "d" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1312 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "e" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 541 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 148 Chain: "f" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 513 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 4, 'TRANS': 68} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 109 Chain: "g" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 525 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 23.67, per 1000 atoms: 0.44 Number of scatterers: 53697 At special positions: 0 Unit cell: (135.247, 171.23, 215.899, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 109 16.00 P 106 15.00 Mg 1 11.99 O 5598 8.00 N 5061 7.00 C 17705 6.00 H 25117 1.00 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: 13.66 Conformation dependent library (CDL) restraints added in 4.3 seconds 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6718 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 30 sheets defined 37.6% alpha, 19.3% beta 32 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 22.78 Creating SS restraints... Processing helix chain 'A' and resid 27 through 45 removed outlier: 4.234A pdb=" N LYS A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS A 43 " --> pdb=" O GLN A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 73 removed outlier: 4.228A pdb=" N VAL A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.949A pdb=" N GLY A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 90' Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 136 through 158 Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.716A pdb=" N ASN A 181 " --> pdb=" O ASP A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 removed outlier: 3.751A pdb=" N LEU A 204 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 309 through 316 removed outlier: 3.725A pdb=" N LYS A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 404 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 427 through 434 removed outlier: 4.660A pdb=" N HIS A 434 " --> pdb=" O TRP A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 460 Processing helix chain 'A' and resid 472 through 479 removed outlier: 3.611A pdb=" N ALA A 478 " --> pdb=" O ARG A 474 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 509 removed outlier: 3.528A pdb=" N CYS A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 541 through 566 removed outlier: 4.012A pdb=" N HIS A 545 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS A 561 " --> pdb=" O VAL A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 584 removed outlier: 3.704A pdb=" N ASP A 576 " --> pdb=" O PHE A 572 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 583 " --> pdb=" O GLN A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 589 Processing helix chain 'A' and resid 590 through 594 removed outlier: 3.643A pdb=" N ARG A 593 " --> pdb=" O GLY A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 617 removed outlier: 3.633A pdb=" N ARG A 603 " --> pdb=" O MET A 599 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 604 " --> pdb=" O ARG A 600 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS A 605 " --> pdb=" O GLN A 601 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR A 613 " --> pdb=" O LYS A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 657 removed outlier: 4.117A pdb=" N VAL A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 680 through 695 Processing helix chain 'A' and resid 698 through 706 removed outlier: 4.198A pdb=" N ASN A 704 " --> pdb=" O GLY A 700 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 722 removed outlier: 4.469A pdb=" N HIS A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER A 714 " --> pdb=" O LEU A 710 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 763 removed outlier: 3.582A pdb=" N ARG A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 798 removed outlier: 3.636A pdb=" N CYS A 772 " --> pdb=" O ASP A 768 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 777 " --> pdb=" O LYS A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 821 removed outlier: 3.526A pdb=" N ALA A 806 " --> pdb=" O THR A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 848 Processing helix chain 'A' and resid 849 through 852 removed outlier: 3.898A pdb=" N VAL A 852 " --> pdb=" O ALA A 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 849 through 852' Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 873 through 887 Processing helix chain 'A' and resid 912 through 933 removed outlier: 4.001A pdb=" N THR A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 961 Processing helix chain 'A' and resid 989 through 998 Processing helix chain 'A' and resid 1002 through 1012 Processing helix chain 'A' and resid 1036 through 1053 removed outlier: 3.614A pdb=" N ILE A1040 " --> pdb=" O PHE A1036 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN A1042 " --> pdb=" O SER A1038 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A1046 " --> pdb=" O GLN A1042 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A1051 " --> pdb=" O VAL A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1063 Processing helix chain 'A' and resid 1102 through 1117 removed outlier: 4.055A pdb=" N GLU A1116 " --> pdb=" O ARG A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1160 removed outlier: 4.017A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1202 No H-bonds generated for 'chain 'A' and resid 1200 through 1202' Processing helix chain 'A' and resid 1233 through 1248 removed outlier: 3.620A pdb=" N MET A1237 " --> pdb=" O ASP A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1272 removed outlier: 3.711A pdb=" N ILE A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1304 removed outlier: 3.653A pdb=" N VAL A1289 " --> pdb=" O LEU A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1316 removed outlier: 3.501A pdb=" N VAL A1315 " --> pdb=" O PRO A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1323 Processing helix chain 'A' and resid 1368 through 1372 removed outlier: 3.597A pdb=" N ILE A1372 " --> pdb=" O TYR A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1399 removed outlier: 3.725A pdb=" N ALA A1398 " --> pdb=" O GLN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1422 Processing helix chain 'A' and resid 1426 through 1431 Processing helix chain 'A' and resid 1435 through 1442 removed outlier: 3.873A pdb=" N ARG A1439 " --> pdb=" O GLY A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1446 Processing helix chain 'A' and resid 1457 through 1462 Processing helix chain 'A' and resid 1467 through 1478 Processing helix chain 'A' and resid 1479 through 1485 removed outlier: 3.517A pdb=" N GLY A1483 " --> pdb=" O GLY A1479 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1488 No H-bonds generated for 'chain 'A' and resid 1486 through 1488' Processing helix chain 'A' and resid 1530 through 1538 Processing helix chain 'A' and resid 1538 through 1543 Processing helix chain 'A' and resid 1566 through 1577 removed outlier: 4.208A pdb=" N SER A1572 " --> pdb=" O THR A1568 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN A1575 " --> pdb=" O ILE A1571 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1599 removed outlier: 3.772A pdb=" N GLN A1599 " --> pdb=" O GLN A1595 " (cutoff:3.500A) Processing helix chain 'A' and resid 1675 through 1688 Processing helix chain 'A' and resid 1721 through 1737 removed outlier: 4.054A pdb=" N LEU A1725 " --> pdb=" O GLY A1721 " (cutoff:3.500A) Processing helix chain 'A' and resid 1737 through 1752 Processing helix chain 'C' and resid 115 through 123 removed outlier: 3.635A pdb=" N MET C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 154 removed outlier: 3.627A pdb=" N PHE C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 178 removed outlier: 3.557A pdb=" N GLN C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 211 Processing helix chain 'C' and resid 212 through 220 removed outlier: 3.707A pdb=" N GLY C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 249 removed outlier: 3.638A pdb=" N LYS C 244 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 264 removed outlier: 3.578A pdb=" N ARG C 262 " --> pdb=" O LYS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 293 removed outlier: 3.991A pdb=" N TYR C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 319 through 331 removed outlier: 3.661A pdb=" N PHE C 323 " --> pdb=" O THR C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 341 through 343 No H-bonds generated for 'chain 'C' and resid 341 through 343' Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 391 through 399 Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.671A pdb=" N LYS C 409 " --> pdb=" O LYS C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 427 through 437 removed outlier: 3.833A pdb=" N VAL C 431 " --> pdb=" O PHE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 453 removed outlier: 3.876A pdb=" N LYS C 448 " --> pdb=" O GLY C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 466 removed outlier: 3.555A pdb=" N ALA C 464 " --> pdb=" O ASP C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 598 No H-bonds generated for 'chain 'C' and resid 596 through 598' Processing helix chain 'C' and resid 599 through 614 removed outlier: 3.523A pdb=" N ASP C 605 " --> pdb=" O PRO C 601 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG C 608 " --> pdb=" O LEU C 604 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN C 611 " --> pdb=" O LEU C 607 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS C 612 " --> pdb=" O ARG C 608 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER C 613 " --> pdb=" O LYS C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 649 Processing helix chain 'C' and resid 695 through 702 Processing helix chain 'C' and resid 711 through 721 removed outlier: 3.780A pdb=" N GLY C 715 " --> pdb=" O ARG C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 730 Processing helix chain 'C' and resid 755 through 775 removed outlier: 4.569A pdb=" N SER C 761 " --> pdb=" O ALA C 757 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL C 762 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASP C 764 " --> pdb=" O GLY C 760 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N SER C 765 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN C 768 " --> pdb=" O ASP C 764 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 823 removed outlier: 3.621A pdb=" N ILE C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) Proline residue: C 810 - end of helix removed outlier: 3.587A pdb=" N ALA C 823 " --> pdb=" O ALA C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 851 Processing helix chain 'C' and resid 882 through 891 Processing helix chain 'C' and resid 925 through 927 No H-bonds generated for 'chain 'C' and resid 925 through 927' Processing helix chain 'C' and resid 928 through 942 Processing helix chain 'F' and resid 100 through 114 Processing helix chain 'F' and resid 116 through 121 removed outlier: 3.759A pdb=" N GLU F 121 " --> pdb=" O LYS F 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 98 Processing helix chain 'G' and resid 153 through 165 Processing helix chain 'G' and resid 170 through 180 Processing helix chain 'G' and resid 195 through 211 Processing helix chain 'G' and resid 221 through 231 Processing helix chain 'H' and resid 86 through 97 Processing helix chain 'a' and resid 3 through 8 removed outlier: 3.504A pdb=" N MET a 8 " --> pdb=" O VAL a 4 " (cutoff:3.500A) Processing helix chain 'a' and resid 75 through 79 removed outlier: 3.648A pdb=" N THR a 78 " --> pdb=" O PRO a 75 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 11 Processing helix chain 'c' and resid 18 through 23 Processing helix chain 'c' and resid 29 through 38 removed outlier: 3.851A pdb=" N THR c 33 " --> pdb=" O LEU c 29 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER c 35 " --> pdb=" O VAL c 31 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 13 removed outlier: 3.896A pdb=" N LYS d 8 " --> pdb=" O GLY d 4 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 84 removed outlier: 3.955A pdb=" N LEU d 77 " --> pdb=" O PRO d 74 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS d 78 " --> pdb=" O ASP d 75 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN d 79 " --> pdb=" O MET d 76 " (cutoff:3.500A) Proline residue: d 81 - end of helix Processing helix chain 'e' and resid 16 through 28 Processing helix chain 'f' and resid 6 through 14 Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 121 Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA4, first strand: chain 'A' and resid 516 through 518 Processing sheet with id=AA5, first strand: chain 'A' and resid 906 through 910 removed outlier: 3.858A pdb=" N VAL A 906 " --> pdb=" O MET A 899 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1085 through 1090 removed outlier: 5.595A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1185 through 1189 Processing sheet with id=AA8, first strand: chain 'A' and resid 1341 through 1346 Processing sheet with id=AA9, first strand: chain 'A' and resid 1502 through 1503 Processing sheet with id=AB1, first strand: chain 'A' and resid 1561 through 1563 removed outlier: 7.765A pdb=" N GLN A1552 " --> pdb=" O ARG G 86 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N THR G 88 " --> pdb=" O GLN A1552 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLN A1554 " --> pdb=" O THR G 88 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1606 through 1611 removed outlier: 8.033A pdb=" N ILE A1606 " --> pdb=" O SER A1634 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N SER A1634 " --> pdb=" O ILE A1606 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR A1608 " --> pdb=" O PHE A1632 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLN A1658 " --> pdb=" O ALA A1633 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 184 through 191 removed outlier: 9.274A pdb=" N GLY C 224 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASN C 131 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL C 226 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR C 133 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N PHE C 228 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N CYS C 135 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ASP C 230 " --> pdb=" O CYS C 135 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 348 through 350 Processing sheet with id=AB5, first strand: chain 'C' and resid 522 through 526 removed outlier: 7.058A pdb=" N CYS C 476 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU C 497 " --> pdb=" O CYS C 476 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N THR C 478 " --> pdb=" O ARG C 495 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ARG C 495 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N TRP C 549 " --> pdb=" O SER C 533 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N SER C 533 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU C 530 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 501 through 502 Processing sheet with id=AB7, first strand: chain 'C' and resid 618 through 621 removed outlier: 4.068A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 618 through 621 removed outlier: 4.068A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 663 through 666 removed outlier: 6.785A pdb=" N PHE C 874 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL C 857 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 663 through 666 removed outlier: 5.542A pdb=" N PHE C 833 " --> pdb=" O PHE C 901 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N PHE C 901 " --> pdb=" O PHE C 833 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLU C 835 " --> pdb=" O SER C 899 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER C 899 " --> pdb=" O GLU C 835 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLN C 837 " --> pdb=" O SER C 897 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N SER C 897 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 674 through 677 removed outlier: 6.565A pdb=" N LYS C 684 " --> pdb=" O ALA C 794 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA C 794 " --> pdb=" O LYS C 684 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR C 686 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 734 " --> pdb=" O LEU C 745 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP C 747 " --> pdb=" O ILE C 732 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE C 732 " --> pdb=" O ASP C 747 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 61 through 63 Processing sheet with id=AC4, first strand: chain 'D' and resid 69 through 74 removed outlier: 4.595A pdb=" N GLY D 85 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA D 103 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASN D 94 " --> pdb=" O ASN D 101 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN D 101 " --> pdb=" O ASN D 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 112 through 117 removed outlier: 6.619A pdb=" N ASP D 137 " --> pdb=" O ARG D 143 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ARG D 143 " --> pdb=" O ASP D 137 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 154 through 159 removed outlier: 3.569A pdb=" N SER D 171 " --> pdb=" O THR D 175 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR D 175 " --> pdb=" O SER D 171 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 196 through 201 removed outlier: 4.264A pdb=" N GLY D 212 " --> pdb=" O ASP D 216 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASP D 216 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL D 219 " --> pdb=" O TYR D 229 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR D 229 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP D 221 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU D 227 " --> pdb=" O ASP D 221 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 238 through 243 removed outlier: 3.592A pdb=" N ALA D 254 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS D 275 " --> pdb=" O VAL D 261 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 291 through 293 removed outlier: 3.595A pdb=" N ALA D 302 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR D 310 " --> pdb=" O ALA D 302 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASP D 313 " --> pdb=" O ILE D 319 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE D 319 " --> pdb=" O ASP D 313 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 330 through 335 Processing sheet with id=AD2, first strand: chain 'G' and resid 99 through 101 Processing sheet with id=AD3, first strand: chain 'a' and resid 14 through 19 removed outlier: 4.219A pdb=" N THR a 28 " --> pdb=" O ALA a 42 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ALA a 42 " --> pdb=" O THR a 28 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N THR a 30 " --> pdb=" O LEU a 40 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU a 40 " --> pdb=" O THR a 30 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL a 32 " --> pdb=" O THR a 38 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N THR a 38 " --> pdb=" O VAL a 32 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLU a 56 " --> pdb=" O ALA a 42 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS a 44 " --> pdb=" O GLN a 54 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLN a 54 " --> pdb=" O LYS a 44 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR a 46 " --> pdb=" O PRO a 52 " (cutoff:3.500A) removed outlier: 14.018A pdb=" N LEU a 55 " --> pdb=" O GLY b 84 " (cutoff:3.500A) removed outlier: 12.093A pdb=" N GLY b 84 " --> pdb=" O LEU a 55 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N THR a 57 " --> pdb=" O VAL b 82 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG b 16 " --> pdb=" O GLU b 83 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N THR b 30 " --> pdb=" O ASP b 44 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASP b 44 " --> pdb=" O THR b 30 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS b 32 " --> pdb=" O LEU b 42 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU b 42 " --> pdb=" O LYS b 32 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE b 41 " --> pdb=" O LEU b 71 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU b 71 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS b 43 " --> pdb=" O LEU b 69 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU b 69 " --> pdb=" O CYS b 43 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N CYS b 45 " --> pdb=" O LEU b 67 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU b 69 " --> pdb=" O LEU d 73 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS d 31 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ASN d 45 " --> pdb=" O LYS d 31 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ILE d 33 " --> pdb=" O MET d 43 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N MET d 43 " --> pdb=" O ILE d 33 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA d 35 " --> pdb=" O CYS d 41 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N CYS d 41 " --> pdb=" O ALA d 35 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLU d 59 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR d 47 " --> pdb=" O GLN d 57 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN d 57 " --> pdb=" O THR d 47 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N THR d 49 " --> pdb=" O VAL d 55 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL d 55 " --> pdb=" O THR d 49 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN d 60 " --> pdb=" O ALA g 72 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS g 20 " --> pdb=" O ILE g 68 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU g 70 " --> pdb=" O SER g 18 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N SER g 18 " --> pdb=" O LEU g 70 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ALA g 72 " --> pdb=" O LYS g 16 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LYS g 16 " --> pdb=" O ALA g 72 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN g 28 " --> pdb=" O CYS g 45 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N CYS g 45 " --> pdb=" O GLN g 28 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL g 41 " --> pdb=" O ARG g 32 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL g 41 " --> pdb=" O VAL g 61 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL g 61 " --> pdb=" O VAL g 41 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP g 43 " --> pdb=" O MET g 59 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N MET g 59 " --> pdb=" O ASP g 43 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N CYS g 45 " --> pdb=" O ILE g 57 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU e 86 " --> pdb=" O TRP e 34 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N CYS e 46 " --> pdb=" O ASP e 60 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASP e 60 " --> pdb=" O CYS e 46 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP e 60 " --> pdb=" O GLY e 75 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLY e 75 " --> pdb=" O ASP e 60 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU e 62 " --> pdb=" O GLN e 73 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLN e 73 " --> pdb=" O GLU e 62 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N MET f 27 " --> pdb=" O LEU f 23 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU f 28 " --> pdb=" O GLU f 49 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU f 49 " --> pdb=" O GLU f 28 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LYS f 30 " --> pdb=" O THR f 47 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR f 47 " --> pdb=" O LYS f 30 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR f 32 " --> pdb=" O ALA f 45 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLN f 43 " --> pdb=" O VAL f 34 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLN f 43 " --> pdb=" O VAL f 62 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL f 62 " --> pdb=" O GLN f 43 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA f 45 " --> pdb=" O GLY f 60 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N GLY f 60 " --> pdb=" O ALA f 45 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N THR f 47 " --> pdb=" O HIS f 58 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N HIS f 58 " --> pdb=" O THR f 47 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N GLU f 49 " --> pdb=" O SER f 56 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU f 61 " --> pdb=" O ARG c 111 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG c 111 " --> pdb=" O GLU f 61 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL c 109 " --> pdb=" O LEU f 63 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS c 51 " --> pdb=" O GLU c 72 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU c 72 " --> pdb=" O LYS c 51 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU c 53 " --> pdb=" O VAL c 70 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL c 70 " --> pdb=" O LEU c 53 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL c 66 " --> pdb=" O LYS c 57 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER c 97 " --> pdb=" O ASN c 69 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LYS c 71 " --> pdb=" O TYR c 95 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR c 95 " --> pdb=" O LYS c 71 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N MET c 73 " --> pdb=" O ASP c 93 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP c 93 " --> pdb=" O MET c 73 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR c 75 " --> pdb=" O ASN c 91 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN c 91 " --> pdb=" O THR c 75 " (cutoff:3.500A) 1199 hydrogen bonds defined for protein. 3420 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 59 stacking parallelities Total time for adding SS restraints: 27.15 Time building geometry restraints manager: 16.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 25080 1.13 - 1.30: 4591 1.30 - 1.47: 12102 1.47 - 1.64: 12540 1.64 - 1.81: 181 Bond restraints: 54494 Sorted by residual: bond pdb=" NH1 ARG A 510 " pdb="HH12 ARG A 510 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CE1 PHE A 540 " pdb=" HE1 PHE A 540 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CZ PHE A1719 " pdb=" HZ PHE A1719 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N2 G 5 37 " pdb=" H22 G 5 37 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" NH1 ARG A 603 " pdb="HH12 ARG A 603 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 54489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.19: 91291 4.19 - 8.37: 6595 8.37 - 12.56: 50 12.56 - 16.74: 3 16.74 - 20.93: 2 Bond angle restraints: 97941 Sorted by residual: angle pdb=" C6 A 5 66 " pdb=" N6 A 5 66 " pdb=" H61 A 5 66 " ideal model delta sigma weight residual 120.00 99.07 20.93 3.00e+00 1.11e-01 4.87e+01 angle pdb=" C GLY H 84 " pdb=" N MET H 85 " pdb=" CA MET H 85 " ideal model delta sigma weight residual 121.31 130.79 -9.48 1.49e+00 4.50e-01 4.05e+01 angle pdb=" N TYR A1091 " pdb=" CA TYR A1091 " pdb=" C TYR A1091 " ideal model delta sigma weight residual 110.53 102.49 8.04 1.29e+00 6.01e-01 3.88e+01 angle pdb=" C6 A 5 19 " pdb=" N6 A 5 19 " pdb=" H61 A 5 19 " ideal model delta sigma weight residual 120.00 101.51 18.49 3.00e+00 1.11e-01 3.80e+01 angle pdb=" CA PHE C 735 " pdb=" CB PHE C 735 " pdb=" CG PHE C 735 " ideal model delta sigma weight residual 113.80 119.91 -6.11 1.00e+00 1.00e+00 3.74e+01 ... (remaining 97936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 25108 35.47 - 70.94: 1006 70.94 - 106.41: 73 106.41 - 141.88: 5 141.88 - 177.35: 6 Dihedral angle restraints: 26198 sinusoidal: 14238 harmonic: 11960 Sorted by residual: dihedral pdb=" CA PHE A 166 " pdb=" C PHE A 166 " pdb=" N PRO A 167 " pdb=" CA PRO A 167 " ideal model delta harmonic sigma weight residual 180.00 -107.93 -72.07 0 5.00e+00 4.00e-02 2.08e+02 dihedral pdb=" C4' U 5 105 " pdb=" C3' U 5 105 " pdb=" C2' U 5 105 " pdb=" C1' U 5 105 " ideal model delta sinusoidal sigma weight residual -35.00 33.70 -68.70 1 8.00e+00 1.56e-02 9.55e+01 dihedral pdb=" C5' U 5 105 " pdb=" C4' U 5 105 " pdb=" C3' U 5 105 " pdb=" O3' U 5 105 " ideal model delta sinusoidal sigma weight residual 147.00 80.20 66.80 1 8.00e+00 1.56e-02 9.09e+01 ... (remaining 26195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4141 0.083 - 0.166: 490 0.166 - 0.249: 31 0.249 - 0.332: 6 0.332 - 0.415: 2 Chirality restraints: 4670 Sorted by residual: chirality pdb=" CA THR C 708 " pdb=" N THR C 708 " pdb=" C THR C 708 " pdb=" CB THR C 708 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" C3' U 5 105 " pdb=" C4' U 5 105 " pdb=" O3' U 5 105 " pdb=" C2' U 5 105 " both_signs ideal model delta sigma weight residual False -2.74 -2.41 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C3' U 5 58 " pdb=" C4' U 5 58 " pdb=" O3' U 5 58 " pdb=" C2' U 5 58 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 4667 not shown) Planarity restraints: 8315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C6 A 5 26 " 0.055 2.00e-02 2.50e+03 1.18e-01 1.39e+02 pdb=" N6 A 5 26 " -0.204 2.00e-02 2.50e+03 pdb=" H61 A 5 26 " 0.075 2.00e-02 2.50e+03 pdb=" H62 A 5 26 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP C1101 " -0.147 2.00e-02 2.50e+03 6.06e-02 1.10e+02 pdb=" C2 GTP C1101 " -0.010 2.00e-02 2.50e+03 pdb=" C4 GTP C1101 " 0.049 2.00e-02 2.50e+03 pdb=" C5 GTP C1101 " 0.035 2.00e-02 2.50e+03 pdb=" C6 GTP C1101 " -0.022 2.00e-02 2.50e+03 pdb=" C8 GTP C1101 " 0.039 2.00e-02 2.50e+03 pdb=" N1 GTP C1101 " -0.018 2.00e-02 2.50e+03 pdb=" N2 GTP C1101 " 0.030 2.00e-02 2.50e+03 pdb=" N3 GTP C1101 " 0.050 2.00e-02 2.50e+03 pdb=" N7 GTP C1101 " 0.058 2.00e-02 2.50e+03 pdb=" N9 GTP C1101 " 0.030 2.00e-02 2.50e+03 pdb=" O6 GTP C1101 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1465 " 0.092 2.00e-02 2.50e+03 4.70e-02 8.84e+01 pdb=" CG TRP A1465 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP A1465 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP A1465 " -0.014 2.00e-02 2.50e+03 pdb=" NE1 TRP A1465 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TRP A1465 " -0.019 2.00e-02 2.50e+03 pdb=" CE3 TRP A1465 " -0.041 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1465 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1465 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A1465 " 0.046 2.00e-02 2.50e+03 pdb=" HD1 TRP A1465 " 0.034 2.00e-02 2.50e+03 pdb=" HE1 TRP A1465 " -0.072 2.00e-02 2.50e+03 pdb=" HE3 TRP A1465 " -0.092 2.00e-02 2.50e+03 pdb=" HZ2 TRP A1465 " 0.004 2.00e-02 2.50e+03 pdb=" HZ3 TRP A1465 " -0.014 2.00e-02 2.50e+03 pdb=" HH2 TRP A1465 " 0.074 2.00e-02 2.50e+03 ... (remaining 8312 not shown) Histogram of nonbonded interaction distances: 1.32 - 1.98: 1284 1.98 - 2.63: 58409 2.63 - 3.29: 147339 3.29 - 3.94: 192743 3.94 - 4.60: 289509 Nonbonded interactions: 689284 Sorted by model distance: nonbonded pdb=" H3 U 5 17 " pdb=" H1 G 5 60 " model vdw 1.323 2.100 nonbonded pdb="HD21 ASN A1184 " pdb="HH11 ARG A1195 " model vdw 1.347 2.100 nonbonded pdb="HH22 ARG A 998 " pdb=" HA PRO H 79 " model vdw 1.371 2.270 nonbonded pdb="HH21 ARG C 853 " pdb=" OD2 ASP C 886 " model vdw 1.375 2.450 nonbonded pdb=" O LEU A 776 " pdb=" HG1 THR A 780 " model vdw 1.384 2.450 ... (remaining 689279 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.450 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: 0.910 Extract box with map and model: 1.830 Check model and map are aligned: 0.370 Set scattering table: 0.440 Process input model: 129.130 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 29377 Z= 0.293 Angle : 0.921 14.426 40452 Z= 0.549 Chirality : 0.053 0.415 4670 Planarity : 0.007 0.111 4894 Dihedral : 13.561 177.352 10995 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.88 % Favored : 95.98 % Rotamer: Outliers : 0.16 % Allowed : 1.44 % Favored : 98.40 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.12), residues: 3505 helix: -2.29 (0.11), residues: 1174 sheet: -0.89 (0.20), residues: 613 loop : -2.05 (0.12), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.004 TRP A1465 HIS 0.008 0.001 HIS A 333 PHE 0.035 0.003 PHE C 770 TYR 0.029 0.002 TYR C 198 ARG 0.010 0.001 ARG C 785 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 140 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue TYR 158 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 213 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue TYR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue MET 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue TYR 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue SER 252 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue VAL 259 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 274 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 281 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue SER 294 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue TYR 310 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue VAL 333 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue SER 346 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue ILE 356 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue VAL 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 8 is missing expected H atoms. Skipping. Residue LYS 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue THR 23 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue VAL 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue TYR 67 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue MET 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue MET 17 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue MET 80 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue LEU 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 26 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue MET 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue MET 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue TYR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue MET 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue THR 15 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue TYR 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue TYR 39 is missing expected H atoms. Skipping. Residue MET 40 is missing expected H atoms. Skipping. Residue MET 42 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 71 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LEU 9 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 17 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue ILE 68 is missing expected H atoms. Skipping. Residue MET 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Evaluate side-chains 534 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 530 time to evaluate : 4.078 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: 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 536 LYS cc_start: 0.7161 (tttt) cc_final: 0.6854 (tmmt) REVERT: A 696 MET cc_start: -0.0257 (tmt) cc_final: -0.0759 (mmm) REVERT: A 1094 ARG cc_start: 0.7808 (mtp180) cc_final: 0.7562 (mtm180) REVERT: A 1728 GLN cc_start: 0.8657 (mt0) cc_final: 0.8379 (mt0) REVERT: A 1732 LYS cc_start: 0.8994 (tttt) cc_final: 0.8548 (tppt) REVERT: C 688 ILE cc_start: 0.7871 (mm) cc_final: 0.7599 (tp) REVERT: C 694 LYS cc_start: 0.8905 (mttt) cc_final: 0.8552 (tptm) REVERT: G 217 VAL cc_start: 0.4412 (m) cc_final: 0.3550 (m) REVERT: G 227 MET cc_start: 0.6051 (mtt) cc_final: 0.5462 (tmm) REVERT: d 70 PHE cc_start: 0.6446 (p90) cc_final: 0.6222 (p90) REVERT: d 71 LEU cc_start: 0.8827 (mp) cc_final: 0.8611 (mp) REVERT: d 76 MET cc_start: 0.8630 (pp-130) cc_final: 0.8268 (pp-130) outliers start: 4 outliers final: 1 residues processed: 533 average time/residue: 1.0938 time to fit residues: 864.3343 Evaluate side-chains 271 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 270 time to evaluate : 4.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 258 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 303 optimal weight: 5.9990 chunk 272 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 281 optimal weight: 30.0000 chunk 108 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 chunk 209 optimal weight: 0.9980 chunk 326 optimal weight: 9.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 253 ASN A 483 GLN A 704 ASN A 793 ASN A1023 ASN A1293 ASN A1367 ASN A1623 ASN A1658 GLN C 201 ASN C 258 ASN C 611 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29377 Z= 0.194 Angle : 0.575 7.970 40452 Z= 0.311 Chirality : 0.042 0.159 4670 Planarity : 0.005 0.084 4894 Dihedral : 15.607 179.829 5432 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.85 % Favored : 97.03 % Rotamer: Outliers : 1.19 % Allowed : 6.23 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.13), residues: 3505 helix: -0.22 (0.14), residues: 1204 sheet: -0.51 (0.20), residues: 618 loop : -1.59 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 406 HIS 0.007 0.001 HIS C 140 PHE 0.025 0.001 PHE A 166 TYR 0.021 0.001 TYR A 431 ARG 0.006 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 140 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue TYR 158 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 213 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue TYR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue MET 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue TYR 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue SER 252 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue VAL 259 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 274 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 281 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue SER 294 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue TYR 310 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue VAL 333 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue SER 346 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue ILE 356 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue VAL 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 8 is missing expected H atoms. Skipping. Residue LYS 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue THR 23 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue VAL 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue TYR 67 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue MET 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue MET 17 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue MET 80 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue LEU 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 26 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue MET 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue MET 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue TYR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue MET 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue THR 15 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue TYR 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue TYR 39 is missing expected H atoms. Skipping. Residue MET 40 is missing expected H atoms. Skipping. Residue MET 42 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 71 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LEU 9 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 17 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue ILE 68 is missing expected H atoms. Skipping. Residue MET 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Evaluate side-chains 310 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 281 time to evaluate : 3.918 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: A 235 MET cc_start: 0.9192 (mmm) cc_final: 0.8789 (mmt) REVERT: A 536 LYS cc_start: 0.6867 (tttt) cc_final: 0.6592 (tmmt) REVERT: A 696 MET cc_start: 0.0151 (tmt) cc_final: -0.0602 (mmm) REVERT: A 1048 MET cc_start: 0.8849 (mmp) cc_final: 0.8253 (mmp) REVERT: A 1732 LYS cc_start: 0.9012 (tttt) cc_final: 0.8582 (tppt) REVERT: C 236 MET cc_start: 0.8597 (mmm) cc_final: 0.8127 (mmp) REVERT: C 694 LYS cc_start: 0.9001 (mttt) cc_final: 0.8627 (tptm) REVERT: C 935 ILE cc_start: 0.8246 (mm) cc_final: 0.7984 (mm) REVERT: G 217 VAL cc_start: 0.3853 (m) cc_final: 0.3637 (m) REVERT: G 227 MET cc_start: 0.6002 (mtt) cc_final: 0.5673 (tmm) REVERT: d 70 PHE cc_start: 0.6528 (p90) cc_final: 0.6235 (p90) REVERT: d 76 MET cc_start: 0.8675 (pp-130) cc_final: 0.8315 (pp-130) outliers start: 29 outliers final: 21 residues processed: 305 average time/residue: 0.7605 time to fit residues: 370.0076 Evaluate side-chains 266 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 245 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 613 TYR Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1353 PHE Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1585 ILE Chi-restraints excluded: chain A residue 1691 ASN Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 608 ARG Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 848 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 181 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 271 optimal weight: 50.0000 chunk 221 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 326 optimal weight: 40.0000 chunk 352 optimal weight: 0.8980 chunk 290 optimal weight: 20.0000 chunk 323 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 262 optimal weight: 30.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1332 HIS A1450 GLN A1712 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29377 Z= 0.230 Angle : 0.559 10.591 40452 Z= 0.299 Chirality : 0.042 0.201 4670 Planarity : 0.005 0.073 4894 Dihedral : 15.351 178.901 5430 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.26 % Rotamer: Outliers : 1.31 % Allowed : 6.81 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3505 helix: 0.70 (0.15), residues: 1214 sheet: -0.40 (0.20), residues: 646 loop : -1.30 (0.14), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 293 HIS 0.007 0.001 HIS C 491 PHE 0.020 0.002 PHE A 166 TYR 0.033 0.002 TYR A 800 ARG 0.005 0.000 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 140 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue TYR 158 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 213 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue TYR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue MET 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue TYR 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue SER 252 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue VAL 259 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 274 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 281 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue SER 294 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue TYR 310 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue VAL 333 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue SER 346 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue ILE 356 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue VAL 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 8 is missing expected H atoms. Skipping. Residue LYS 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue THR 23 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue VAL 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue TYR 67 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue MET 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue MET 17 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue MET 80 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue LEU 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 26 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue MET 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue MET 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue TYR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue MET 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue THR 15 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue TYR 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue TYR 39 is missing expected H atoms. Skipping. Residue MET 40 is missing expected H atoms. Skipping. Residue MET 42 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 71 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LEU 9 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 17 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue ILE 68 is missing expected H atoms. Skipping. Residue MET 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 251 time to evaluate : 4.141 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: A 235 MET cc_start: 0.9159 (mmm) cc_final: 0.8744 (mmt) REVERT: A 536 LYS cc_start: 0.6940 (tttt) cc_final: 0.6587 (tmmt) REVERT: A 696 MET cc_start: 0.0283 (tmt) cc_final: -0.0511 (mmm) REVERT: A 1048 MET cc_start: 0.8889 (mmp) cc_final: 0.8598 (mmp) REVERT: A 1732 LYS cc_start: 0.8916 (tttt) cc_final: 0.8493 (tppt) REVERT: C 694 LYS cc_start: 0.9117 (mttt) cc_final: 0.8757 (tptm) REVERT: C 935 ILE cc_start: 0.8381 (mm) cc_final: 0.8147 (mm) REVERT: d 70 PHE cc_start: 0.6751 (p90) cc_final: 0.6436 (p90) REVERT: d 76 MET cc_start: 0.8756 (pp-130) cc_final: 0.8441 (pp-130) outliers start: 32 outliers final: 21 residues processed: 275 average time/residue: 0.8772 time to fit residues: 385.8259 Evaluate side-chains 247 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 226 time to evaluate : 4.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1644 LEU Chi-restraints excluded: chain A residue 1691 ASN Chi-restraints excluded: chain A residue 1725 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 608 ARG Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain d residue 22 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 322 optimal weight: 30.0000 chunk 245 optimal weight: 9.9990 chunk 169 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 219 optimal weight: 0.4980 chunk 327 optimal weight: 30.0000 chunk 347 optimal weight: 50.0000 chunk 171 optimal weight: 10.0000 chunk 310 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1367 ASN ** A1563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1658 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 29377 Z= 0.445 Angle : 0.669 12.181 40452 Z= 0.360 Chirality : 0.046 0.219 4670 Planarity : 0.006 0.078 4894 Dihedral : 15.384 176.242 5430 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.19 % Favored : 94.75 % Rotamer: Outliers : 1.60 % Allowed : 8.00 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.14), residues: 3505 helix: 0.48 (0.15), residues: 1230 sheet: -0.59 (0.20), residues: 629 loop : -1.47 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 293 HIS 0.014 0.002 HIS C 139 PHE 0.038 0.003 PHE C 339 TYR 0.023 0.002 TYR A 225 ARG 0.009 0.001 ARG A1086 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 140 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue TYR 158 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 213 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue TYR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue MET 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue TYR 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue SER 252 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue VAL 259 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 274 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 281 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue SER 294 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue TYR 310 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue VAL 333 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue SER 346 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue ILE 356 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue VAL 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 8 is missing expected H atoms. Skipping. Residue LYS 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue THR 23 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue VAL 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue TYR 67 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue MET 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue MET 17 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue MET 80 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue LEU 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 26 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue MET 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue MET 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue TYR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue MET 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue THR 15 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue TYR 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue TYR 39 is missing expected H atoms. Skipping. Residue MET 40 is missing expected H atoms. Skipping. Residue MET 42 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 71 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LEU 9 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 17 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue ILE 68 is missing expected H atoms. Skipping. Residue MET 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 224 time to evaluate : 4.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 696 MET cc_start: 0.0747 (tmt) cc_final: -0.0197 (mmt) REVERT: A 848 GLU cc_start: 0.7739 (tt0) cc_final: 0.7528 (tp30) REVERT: A 1328 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8758 (mm) REVERT: A 1732 LYS cc_start: 0.8965 (tttt) cc_final: 0.8519 (tppt) REVERT: C 694 LYS cc_start: 0.9234 (mttt) cc_final: 0.8901 (tptm) REVERT: H 85 MET cc_start: 0.3086 (mpp) cc_final: 0.2830 (mpp) REVERT: d 76 MET cc_start: 0.8897 (pp-130) cc_final: 0.8442 (pp-130) outliers start: 39 outliers final: 29 residues processed: 250 average time/residue: 0.8849 time to fit residues: 355.0414 Evaluate side-chains 237 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 4.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1585 ILE Chi-restraints excluded: chain A residue 1591 MET Chi-restraints excluded: chain A residue 1604 LEU Chi-restraints excluded: chain A residue 1652 MET Chi-restraints excluded: chain A residue 1691 ASN Chi-restraints excluded: chain A residue 1725 LEU Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 608 ARG Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain d residue 22 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 289 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 258 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 296 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 177 optimal weight: 2.9990 chunk 311 optimal weight: 50.0000 chunk 87 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1367 ASN ** A1563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29377 Z= 0.289 Angle : 0.561 7.810 40452 Z= 0.300 Chirality : 0.042 0.150 4670 Planarity : 0.005 0.079 4894 Dihedral : 15.227 178.447 5430 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.31 % Favored : 95.63 % Rotamer: Outliers : 1.31 % Allowed : 8.86 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3505 helix: 0.87 (0.15), residues: 1234 sheet: -0.59 (0.20), residues: 601 loop : -1.35 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 293 HIS 0.005 0.001 HIS A1674 PHE 0.022 0.002 PHE A 166 TYR 0.017 0.002 TYR A 431 ARG 0.004 0.001 ARG A 820 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 140 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue TYR 158 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 213 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue TYR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue MET 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue TYR 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue SER 252 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue VAL 259 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 274 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 281 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue SER 294 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue TYR 310 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue VAL 333 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue SER 346 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue ILE 356 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue VAL 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 8 is missing expected H atoms. Skipping. Residue LYS 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue THR 23 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue VAL 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue TYR 67 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue MET 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue MET 17 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue MET 80 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue LEU 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 26 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue MET 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue MET 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue TYR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue MET 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue THR 15 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue TYR 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue TYR 39 is missing expected H atoms. Skipping. Residue MET 40 is missing expected H atoms. Skipping. Residue MET 42 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 71 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LEU 9 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 17 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue ILE 68 is missing expected H atoms. Skipping. Residue MET 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 4.094 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 147 MET cc_start: 0.8596 (mmp) cc_final: 0.8066 (mmp) REVERT: A 235 MET cc_start: 0.9200 (mmm) cc_final: 0.8955 (mmm) REVERT: A 696 MET cc_start: 0.0715 (tmt) cc_final: -0.0212 (mmt) REVERT: A 848 GLU cc_start: 0.7678 (tt0) cc_final: 0.7462 (tp30) REVERT: A 1237 MET cc_start: 0.9029 (mtp) cc_final: 0.8819 (mtp) REVERT: A 1307 MET cc_start: 0.7990 (tpp) cc_final: 0.7778 (tpp) REVERT: A 1689 THR cc_start: 0.8068 (m) cc_final: 0.7734 (p) REVERT: A 1732 LYS cc_start: 0.9004 (tttt) cc_final: 0.8607 (tppt) REVERT: C 694 LYS cc_start: 0.9254 (mttt) cc_final: 0.8895 (tptm) REVERT: C 935 ILE cc_start: 0.8328 (mm) cc_final: 0.8126 (mm) REVERT: H 91 GLN cc_start: 0.7242 (mm-40) cc_final: 0.6978 (pt0) REVERT: d 67 LYS cc_start: 0.8471 (mmtt) cc_final: 0.8158 (mmtp) REVERT: d 70 PHE cc_start: 0.6973 (p90) cc_final: 0.6494 (p90) outliers start: 32 outliers final: 25 residues processed: 247 average time/residue: 0.8612 time to fit residues: 342.6096 Evaluate side-chains 234 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 4.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1428 HIS Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1585 ILE Chi-restraints excluded: chain A residue 1591 MET Chi-restraints excluded: chain A residue 1604 LEU Chi-restraints excluded: chain A residue 1644 LEU Chi-restraints excluded: chain A residue 1725 LEU Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 608 ARG Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain d residue 22 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 116 optimal weight: 2.9990 chunk 312 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 347 optimal weight: 30.0000 chunk 288 optimal weight: 40.0000 chunk 160 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 182 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29377 Z= 0.167 Angle : 0.505 9.057 40452 Z= 0.267 Chirality : 0.040 0.150 4670 Planarity : 0.004 0.073 4894 Dihedral : 15.018 179.000 5430 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.05 % Favored : 95.89 % Rotamer: Outliers : 1.27 % Allowed : 9.18 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3505 helix: 1.34 (0.15), residues: 1238 sheet: -0.50 (0.20), residues: 628 loop : -1.13 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 720 HIS 0.003 0.001 HIS C 928 PHE 0.021 0.001 PHE A 166 TYR 0.015 0.001 TYR A 431 ARG 0.003 0.000 ARG A1090 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 140 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue TYR 158 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 213 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue TYR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue MET 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue TYR 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue SER 252 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue VAL 259 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 274 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 281 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue SER 294 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue TYR 310 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue VAL 333 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue SER 346 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue ILE 356 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue VAL 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 8 is missing expected H atoms. Skipping. Residue LYS 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue THR 23 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue VAL 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue TYR 67 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue MET 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue MET 17 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue MET 80 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue LEU 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 26 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue MET 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue MET 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue TYR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue MET 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue THR 15 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue TYR 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue TYR 39 is missing expected H atoms. Skipping. Residue MET 40 is missing expected H atoms. Skipping. Residue MET 42 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 71 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LEU 9 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 17 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue ILE 68 is missing expected H atoms. Skipping. Residue MET 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Evaluate side-chains 249 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 4.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.8567 (mmp) cc_final: 0.8060 (mmp) REVERT: A 696 MET cc_start: 0.0761 (tmt) cc_final: -0.0240 (mmt) REVERT: A 848 GLU cc_start: 0.7597 (tt0) cc_final: 0.7391 (tp30) REVERT: A 1394 GLN cc_start: 0.7130 (mm110) cc_final: 0.6930 (mm110) REVERT: A 1689 THR cc_start: 0.8041 (m) cc_final: 0.7727 (p) REVERT: A 1692 MET cc_start: 0.7781 (tpp) cc_final: 0.7520 (ttt) REVERT: A 1732 LYS cc_start: 0.8980 (tttt) cc_final: 0.8530 (tppt) REVERT: C 694 LYS cc_start: 0.9268 (mttt) cc_final: 0.8907 (tptm) REVERT: C 786 ASN cc_start: 0.8373 (t0) cc_final: 0.8002 (t0) REVERT: C 935 ILE cc_start: 0.8362 (mm) cc_final: 0.8099 (mm) REVERT: H 91 GLN cc_start: 0.7251 (mm-40) cc_final: 0.6985 (pt0) REVERT: d 70 PHE cc_start: 0.6881 (p90) cc_final: 0.6414 (p90) outliers start: 31 outliers final: 27 residues processed: 242 average time/residue: 0.8664 time to fit residues: 344.4449 Evaluate side-chains 240 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 3.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1591 MET Chi-restraints excluded: chain A residue 1725 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 608 ARG Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain d residue 68 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 334 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 292 optimal weight: 8.9990 chunk 193 optimal weight: 1.9990 chunk 346 optimal weight: 30.0000 chunk 216 optimal weight: 1.9990 chunk 210 optimal weight: 0.6980 chunk 159 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29377 Z= 0.180 Angle : 0.499 7.944 40452 Z= 0.264 Chirality : 0.040 0.148 4670 Planarity : 0.004 0.071 4894 Dihedral : 14.925 179.052 5430 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.02 % Favored : 95.92 % Rotamer: Outliers : 1.11 % Allowed : 9.59 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3505 helix: 1.51 (0.15), residues: 1239 sheet: -0.45 (0.20), residues: 628 loop : -1.02 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 293 HIS 0.004 0.001 HIS A1674 PHE 0.023 0.001 PHE A 166 TYR 0.014 0.001 TYR A 431 ARG 0.004 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 140 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue TYR 158 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 213 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue TYR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue MET 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue TYR 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue SER 252 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue VAL 259 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 274 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 281 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue SER 294 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue TYR 310 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue VAL 333 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue SER 346 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue ILE 356 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue VAL 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 8 is missing expected H atoms. Skipping. Residue LYS 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue THR 23 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue VAL 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue TYR 67 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue MET 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue MET 17 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue MET 80 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue LEU 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 26 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue MET 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue MET 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue TYR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue MET 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue THR 15 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue TYR 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue TYR 39 is missing expected H atoms. Skipping. Residue MET 40 is missing expected H atoms. Skipping. Residue MET 42 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 71 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LEU 9 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 17 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue ILE 68 is missing expected H atoms. Skipping. Residue MET 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Evaluate side-chains 249 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 222 time to evaluate : 3.933 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 147 MET cc_start: 0.8594 (mmp) cc_final: 0.8119 (mmp) REVERT: A 696 MET cc_start: 0.0754 (tmt) cc_final: -0.0239 (mmt) REVERT: A 848 GLU cc_start: 0.7630 (tt0) cc_final: 0.7409 (tp30) REVERT: A 1689 THR cc_start: 0.8047 (m) cc_final: 0.7745 (p) REVERT: A 1692 MET cc_start: 0.7813 (tpp) cc_final: 0.7583 (ttt) REVERT: A 1728 GLN cc_start: 0.8770 (mt0) cc_final: 0.8211 (mt0) REVERT: A 1732 LYS cc_start: 0.8966 (tttt) cc_final: 0.8556 (tppt) REVERT: C 694 LYS cc_start: 0.9281 (mttt) cc_final: 0.8934 (tptm) REVERT: C 786 ASN cc_start: 0.8405 (t0) cc_final: 0.8079 (t0) REVERT: C 935 ILE cc_start: 0.8360 (mm) cc_final: 0.8111 (mm) REVERT: H 91 GLN cc_start: 0.7254 (mm-40) cc_final: 0.7031 (pt0) REVERT: d 70 PHE cc_start: 0.6889 (p90) cc_final: 0.6465 (p90) outliers start: 27 outliers final: 24 residues processed: 240 average time/residue: 0.9173 time to fit residues: 360.0288 Evaluate side-chains 236 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 212 time to evaluate : 4.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1591 MET Chi-restraints excluded: chain A residue 1652 MET Chi-restraints excluded: chain A residue 1725 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 608 ARG Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain d residue 68 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 214 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 206 optimal weight: 0.3980 chunk 104 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 235 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 271 optimal weight: 30.0000 chunk 314 optimal weight: 20.0000 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1367 ASN ** A1563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29377 Z= 0.254 Angle : 0.528 8.370 40452 Z= 0.280 Chirality : 0.041 0.273 4670 Planarity : 0.004 0.069 4894 Dihedral : 14.921 179.126 5430 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.95 % Rotamer: Outliers : 1.19 % Allowed : 9.96 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3505 helix: 1.45 (0.15), residues: 1250 sheet: -0.51 (0.20), residues: 635 loop : -1.10 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 293 HIS 0.005 0.001 HIS A1580 PHE 0.024 0.002 PHE A 166 TYR 0.014 0.001 TYR A 431 ARG 0.004 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 140 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue TYR 158 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 213 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue TYR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue MET 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue TYR 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue SER 252 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue VAL 259 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 274 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 281 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue SER 294 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue TYR 310 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue VAL 333 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue SER 346 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue ILE 356 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue VAL 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 8 is missing expected H atoms. Skipping. Residue LYS 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue THR 23 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue VAL 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue TYR 67 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue MET 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue MET 17 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue MET 80 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue LEU 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 26 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue MET 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue MET 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue TYR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue MET 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue THR 15 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue TYR 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue TYR 39 is missing expected H atoms. Skipping. Residue MET 40 is missing expected H atoms. Skipping. Residue MET 42 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 71 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LEU 9 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 17 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue ILE 68 is missing expected H atoms. Skipping. Residue MET 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Evaluate side-chains 245 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 3.995 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 147 MET cc_start: 0.8650 (mmp) cc_final: 0.8074 (mmp) REVERT: A 467 GLN cc_start: 0.4352 (pt0) cc_final: 0.3886 (mm-40) REVERT: A 696 MET cc_start: 0.0830 (tmt) cc_final: -0.0229 (mmm) REVERT: A 848 GLU cc_start: 0.7662 (tt0) cc_final: 0.7407 (tp30) REVERT: A 1689 THR cc_start: 0.8156 (m) cc_final: 0.7936 (p) REVERT: A 1692 MET cc_start: 0.7860 (tpp) cc_final: 0.7479 (ttm) REVERT: A 1728 GLN cc_start: 0.8737 (mt0) cc_final: 0.8120 (mt0) REVERT: A 1732 LYS cc_start: 0.8949 (tttt) cc_final: 0.8425 (mmmt) REVERT: C 694 LYS cc_start: 0.9285 (mttt) cc_final: 0.8992 (tptm) REVERT: C 786 ASN cc_start: 0.8406 (t0) cc_final: 0.8150 (t0) REVERT: C 935 ILE cc_start: 0.8369 (mm) cc_final: 0.8108 (mm) REVERT: H 91 GLN cc_start: 0.7358 (mm-40) cc_final: 0.7061 (pt0) REVERT: d 70 PHE cc_start: 0.6979 (p90) cc_final: 0.6565 (p90) outliers start: 29 outliers final: 27 residues processed: 235 average time/residue: 0.8857 time to fit residues: 342.6332 Evaluate side-chains 240 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 4.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1591 MET Chi-restraints excluded: chain A residue 1652 MET Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain d residue 68 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 331 optimal weight: 3.9990 chunk 302 optimal weight: 10.0000 chunk 322 optimal weight: 40.0000 chunk 194 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 291 optimal weight: 10.0000 chunk 304 optimal weight: 4.9990 chunk 321 optimal weight: 0.7980 chunk 211 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN A1367 ASN A1458 GLN ** A1563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 29377 Z= 0.293 Angle : 0.555 9.513 40452 Z= 0.296 Chirality : 0.042 0.154 4670 Planarity : 0.004 0.073 4894 Dihedral : 14.960 179.874 5430 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.25 % Favored : 94.69 % Rotamer: Outliers : 1.23 % Allowed : 10.05 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3505 helix: 1.28 (0.15), residues: 1250 sheet: -0.44 (0.20), residues: 637 loop : -1.20 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 293 HIS 0.008 0.001 HIS A1674 PHE 0.026 0.002 PHE A 166 TYR 0.021 0.002 TYR A1204 ARG 0.004 0.000 ARG A 548 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 140 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue TYR 158 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 213 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue TYR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue MET 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue TYR 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue SER 252 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue VAL 259 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 274 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 281 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue SER 294 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue TYR 310 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue VAL 333 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue SER 346 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue ILE 356 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue VAL 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 8 is missing expected H atoms. Skipping. Residue LYS 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue THR 23 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue VAL 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue TYR 67 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue MET 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue MET 17 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue MET 80 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue LEU 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 26 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue MET 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue MET 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue TYR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue MET 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue THR 15 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue TYR 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue TYR 39 is missing expected H atoms. Skipping. Residue MET 40 is missing expected H atoms. Skipping. Residue MET 42 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 71 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LEU 9 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 17 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue ILE 68 is missing expected H atoms. Skipping. Residue MET 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Evaluate side-chains 244 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 4.069 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: A 147 MET cc_start: 0.8659 (mmp) cc_final: 0.8021 (mmp) REVERT: A 696 MET cc_start: 0.0830 (tmt) cc_final: -0.0280 (mmt) REVERT: A 848 GLU cc_start: 0.7637 (tt0) cc_final: 0.7268 (tp30) REVERT: A 1204 TYR cc_start: 0.6738 (p90) cc_final: 0.6304 (t80) REVERT: A 1689 THR cc_start: 0.8250 (m) cc_final: 0.8022 (p) REVERT: A 1692 MET cc_start: 0.8005 (tpp) cc_final: 0.7587 (ttm) REVERT: A 1728 GLN cc_start: 0.8763 (mt0) cc_final: 0.8177 (mt0) REVERT: A 1732 LYS cc_start: 0.8965 (tttt) cc_final: 0.8419 (mmmt) REVERT: C 694 LYS cc_start: 0.9308 (mttt) cc_final: 0.9014 (tptm) REVERT: C 770 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.6993 (t80) REVERT: C 786 ASN cc_start: 0.8574 (t0) cc_final: 0.8259 (t0) REVERT: C 935 ILE cc_start: 0.8372 (mm) cc_final: 0.8117 (mm) REVERT: H 91 GLN cc_start: 0.7308 (mm-40) cc_final: 0.7042 (pt0) REVERT: d 70 PHE cc_start: 0.7547 (p90) cc_final: 0.6940 (p90) outliers start: 30 outliers final: 24 residues processed: 232 average time/residue: 0.8481 time to fit residues: 321.2368 Evaluate side-chains 233 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 3.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1604 LEU Chi-restraints excluded: chain A residue 1652 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain d residue 68 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 340 optimal weight: 40.0000 chunk 208 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 357 optimal weight: 30.0000 chunk 329 optimal weight: 50.0000 chunk 284 optimal weight: 40.0000 chunk 29 optimal weight: 0.9990 chunk 219 optimal weight: 0.0470 chunk 174 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1367 ASN ** A1563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29377 Z= 0.218 Angle : 0.525 13.127 40452 Z= 0.277 Chirality : 0.041 0.151 4670 Planarity : 0.004 0.072 4894 Dihedral : 14.886 178.633 5430 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.94 % Favored : 95.04 % Rotamer: Outliers : 1.07 % Allowed : 10.29 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3505 helix: 1.46 (0.15), residues: 1253 sheet: -0.48 (0.20), residues: 649 loop : -1.12 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 293 HIS 0.006 0.001 HIS A 434 PHE 0.023 0.001 PHE A 166 TYR 0.015 0.001 TYR A 431 ARG 0.004 0.000 ARG A 548 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 25 is missing expected H atoms. Skipping. Residue SER 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LEU 30 is missing expected H atoms. Skipping. Residue LYS 33 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue TYR 45 is missing expected H atoms. Skipping. Residue SER 53 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue ILE 59 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 61 is missing expected H atoms. Skipping. Residue LEU 62 is missing expected H atoms. Skipping. Residue SER 63 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Residue LYS 73 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LEU 81 is missing expected H atoms. Skipping. Residue SER 83 is missing expected H atoms. Skipping. Residue LEU 89 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue VAL 95 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue TYR 102 is missing expected H atoms. Skipping. Residue THR 104 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 106 is missing expected H atoms. Skipping. Residue SER 109 is missing expected H atoms. Skipping. Residue VAL 112 is missing expected H atoms. Skipping. Residue MET 113 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue SER 122 is missing expected H atoms. Skipping. Residue MET 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue SER 126 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue THR 129 is missing expected H atoms. Skipping. Residue LYS 131 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue VAL 133 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 138 is missing expected H atoms. Skipping. Residue THR 140 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LEU 147 is missing expected H atoms. Skipping. Residue LYS 148 is missing expected H atoms. Skipping. Residue THR 151 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue VAL 154 is missing expected H atoms. Skipping. Residue SER 156 is missing expected H atoms. Skipping. Residue TYR 158 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue VAL 167 is missing expected H atoms. Skipping. Residue THR 169 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LEU 178 is missing expected H atoms. Skipping. Residue ILE 181 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue LYS 184 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue THR 189 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue TYR 194 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue VAL 199 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue THR 204 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue ILE 208 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue SER 210 is missing expected H atoms. Skipping. Residue ILE 213 is missing expected H atoms. Skipping. Residue ILE 217 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue VAL 219 is missing expected H atoms. Skipping. Residue LEU 222 is missing expected H atoms. Skipping. Residue LYS 226 is missing expected H atoms. Skipping. Residue LEU 227 is missing expected H atoms. Skipping. Residue THR 228 is missing expected H atoms. Skipping. Residue TYR 229 is missing expected H atoms. Skipping. Residue THR 230 is missing expected H atoms. Skipping. Residue MET 231 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue VAL 238 is missing expected H atoms. Skipping. Residue THR 239 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue SER 242 is missing expected H atoms. Skipping. Residue LEU 243 is missing expected H atoms. Skipping. Residue SER 244 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue TYR 249 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue LEU 251 is missing expected H atoms. Skipping. Residue SER 252 is missing expected H atoms. Skipping. Residue MET 255 is missing expected H atoms. Skipping. Residue THR 258 is missing expected H atoms. Skipping. Residue VAL 259 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue VAL 264 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 274 is missing expected H atoms. Skipping. Residue LYS 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue VAL 281 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue LEU 289 is missing expected H atoms. Skipping. Residue SER 292 is missing expected H atoms. Skipping. Residue SER 294 is missing expected H atoms. Skipping. Residue SER 298 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue ILE 300 is missing expected H atoms. Skipping. Residue SER 304 is missing expected H atoms. Skipping. Residue VAL 309 is missing expected H atoms. Skipping. Residue TYR 310 is missing expected H atoms. Skipping. Residue VAL 311 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue THR 315 is missing expected H atoms. Skipping. Residue SER 316 is missing expected H atoms. Skipping. Residue ILE 319 is missing expected H atoms. Skipping. Residue LEU 320 is missing expected H atoms. Skipping. Residue TYR 321 is missing expected H atoms. Skipping. Residue LYS 322 is missing expected H atoms. Skipping. Residue LEU 323 is missing expected H atoms. Skipping. Residue SER 329 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue VAL 333 is missing expected H atoms. Skipping. Residue ILE 341 is missing expected H atoms. Skipping. Residue ILE 342 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue SER 344 is missing expected H atoms. Skipping. Residue SER 346 is missing expected H atoms. Skipping. Residue SER 347 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue LEU 351 is missing expected H atoms. Skipping. Residue TYR 352 is missing expected H atoms. Skipping. Residue MET 353 is missing expected H atoms. Skipping. Residue ILE 356 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue TYR 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue MET 112 is missing expected H atoms. Skipping. Residue LYS 117 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue VAL 4 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue MET 8 is missing expected H atoms. Skipping. Residue LYS 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue THR 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Residue ILE 17 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue THR 23 is missing expected H atoms. Skipping. Residue VAL 25 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue VAL 32 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue MET 36 is missing expected H atoms. Skipping. Residue THR 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue VAL 43 is missing expected H atoms. Skipping. Residue LYS 44 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue THR 46 is missing expected H atoms. Skipping. Residue LEU 47 is missing expected H atoms. Skipping. Residue LYS 48 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue THR 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue SER 59 is missing expected H atoms. Skipping. Residue ILE 60 is missing expected H atoms. Skipping. Residue ILE 65 is missing expected H atoms. Skipping. Residue TYR 67 is missing expected H atoms. Skipping. Residue ILE 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue LEU 76 is missing expected H atoms. Skipping. Residue THR 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LEU 80 is missing expected H atoms. Skipping. Residue VAL 81 is missing expected H atoms. Skipping. Residue SER 6 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue MET 9 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue ILE 13 is missing expected H atoms. Skipping. Residue TYR 15 is missing expected H atoms. Skipping. Residue MET 17 is missing expected H atoms. Skipping. Residue ILE 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue LEU 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue LEU 69 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue LEU 72 is missing expected H atoms. Skipping. Residue LEU 77 is missing expected H atoms. Skipping. Residue VAL 78 is missing expected H atoms. Skipping. Residue SER 79 is missing expected H atoms. Skipping. Residue MET 80 is missing expected H atoms. Skipping. Residue THR 81 is missing expected H atoms. Skipping. Residue VAL 82 is missing expected H atoms. Skipping. Residue MET 11 is missing expected H atoms. Skipping. Residue THR 12 is missing expected H atoms. Skipping. Residue LEU 16 is missing expected H atoms. Skipping. Residue LYS 18 is missing expected H atoms. Skipping. Residue THR 26 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue VAL 31 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 33 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LEU 43 is missing expected H atoms. Skipping. Residue ILE 44 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LEU 52 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue MET 65 is missing expected H atoms. Skipping. Residue VAL 66 is missing expected H atoms. Skipping. Residue LEU 67 is missing expected H atoms. Skipping. Residue VAL 70 is missing expected H atoms. Skipping. Residue LYS 71 is missing expected H atoms. Skipping. Residue MET 73 is missing expected H atoms. Skipping. Residue THR 75 is missing expected H atoms. Skipping. Residue VAL 77 is missing expected H atoms. Skipping. Residue SER 87 is missing expected H atoms. Skipping. Residue LYS 88 is missing expected H atoms. Skipping. Residue VAL 90 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Residue TYR 95 is missing expected H atoms. Skipping. Residue ILE 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 98 is missing expected H atoms. Skipping. Residue MET 99 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue ILE 107 is missing expected H atoms. Skipping. Residue VAL 108 is missing expected H atoms. Skipping. Residue VAL 109 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 114 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue MET 14 is missing expected H atoms. Skipping. Residue VAL 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LEU 20 is missing expected H atoms. Skipping. Residue ILE 21 is missing expected H atoms. Skipping. Residue TYR 24 is missing expected H atoms. Skipping. Residue LEU 25 is missing expected H atoms. Skipping. Residue SER 29 is missing expected H atoms. Skipping. Residue ILE 31 is missing expected H atoms. Skipping. Residue VAL 33 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue TYR 36 is missing expected H atoms. Skipping. Residue VAL 39 is missing expected H atoms. Skipping. Residue MET 41 is missing expected H atoms. Skipping. Residue ILE 43 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue ILE 48 is missing expected H atoms. Skipping. Residue TYR 53 is missing expected H atoms. Skipping. Residue MET 54 is missing expected H atoms. Skipping. Residue LEU 56 is missing expected H atoms. Skipping. Residue VAL 57 is missing expected H atoms. Skipping. Residue LEU 58 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue THR 68 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue SER 70 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue ILE 77 is missing expected H atoms. Skipping. Residue MET 78 is missing expected H atoms. Skipping. Residue LEU 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue ILE 84 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LEU 86 is missing expected H atoms. Skipping. Residue LEU 87 is missing expected H atoms. Skipping. Residue SER 89 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LYS 8 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue THR 15 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue MET 20 is missing expected H atoms. Skipping. Residue VAL 21 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 23 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue MET 27 is missing expected H atoms. Skipping. Residue TYR 29 is missing expected H atoms. Skipping. Residue LYS 30 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue SER 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue TYR 39 is missing expected H atoms. Skipping. Residue MET 40 is missing expected H atoms. Skipping. Residue MET 42 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 47 is missing expected H atoms. Skipping. Residue TYR 50 is missing expected H atoms. Skipping. Residue ILE 51 is missing expected H atoms. Skipping. Residue LEU 55 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LEU 59 is missing expected H atoms. Skipping. Residue VAL 62 is missing expected H atoms. Skipping. Residue LEU 63 is missing expected H atoms. Skipping. Residue ILE 64 is missing expected H atoms. Skipping. Residue VAL 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 71 is missing expected H atoms. Skipping. Residue ILE 72 is missing expected H atoms. Skipping. Residue LYS 3 is missing expected H atoms. Skipping. Residue LEU 9 is missing expected H atoms. Skipping. Residue LYS 10 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue MET 13 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 16 is missing expected H atoms. Skipping. Residue LEU 17 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue VAL 27 is missing expected H atoms. Skipping. Residue ILE 30 is missing expected H atoms. Skipping. Residue LEU 31 is missing expected H atoms. Skipping. Residue MET 38 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue VAL 41 is missing expected H atoms. Skipping. Residue ILE 42 is missing expected H atoms. Skipping. Residue VAL 46 is missing expected H atoms. Skipping. Residue MET 48 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue MET 59 is missing expected H atoms. Skipping. Residue VAL 60 is missing expected H atoms. Skipping. Residue VAL 61 is missing expected H atoms. Skipping. Residue ILE 62 is missing expected H atoms. Skipping. Residue SER 66 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue ILE 68 is missing expected H atoms. Skipping. Residue MET 69 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue LEU 73 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 4.069 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: A 147 MET cc_start: 0.8694 (mmp) cc_final: 0.8111 (mmp) REVERT: A 467 GLN cc_start: 0.4733 (pt0) cc_final: 0.4046 (mm-40) REVERT: A 696 MET cc_start: 0.0829 (tmt) cc_final: -0.0254 (mmt) REVERT: A 848 GLU cc_start: 0.7822 (tt0) cc_final: 0.7453 (tp30) REVERT: A 1205 GLU cc_start: 0.6043 (tp30) cc_final: 0.5360 (mt-10) REVERT: A 1689 THR cc_start: 0.8237 (m) cc_final: 0.8018 (p) REVERT: A 1728 GLN cc_start: 0.8756 (mt0) cc_final: 0.8200 (mt0) REVERT: A 1732 LYS cc_start: 0.8954 (tttt) cc_final: 0.8570 (mmmt) REVERT: C 694 LYS cc_start: 0.9276 (mttt) cc_final: 0.8995 (tptm) REVERT: C 770 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.6993 (t80) REVERT: C 786 ASN cc_start: 0.8554 (t0) cc_final: 0.8161 (t0) REVERT: C 935 ILE cc_start: 0.8371 (mm) cc_final: 0.8115 (mm) REVERT: H 91 GLN cc_start: 0.7353 (mm-40) cc_final: 0.7069 (pt0) REVERT: d 70 PHE cc_start: 0.7238 (p90) cc_final: 0.6644 (p90) outliers start: 26 outliers final: 25 residues processed: 230 average time/residue: 0.8205 time to fit residues: 311.5207 Evaluate side-chains 238 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 4.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 871 TYR Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1030 ILE Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1070 ASP Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1281 THR Chi-restraints excluded: chain A residue 1329 SER Chi-restraints excluded: chain A residue 1334 LEU Chi-restraints excluded: chain A residue 1429 THR Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1604 LEU Chi-restraints excluded: chain A residue 1635 TYR Chi-restraints excluded: chain A residue 1652 MET Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain d residue 68 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 359 random chunks: chunk 303 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 262 optimal weight: 40.0000 chunk 42 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 285 optimal weight: 30.0000 chunk 119 optimal weight: 3.9990 chunk 292 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 250 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1145 HIS A1367 ASN ** A1563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.132651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.093150 restraints weight = 181283.989| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.16 r_work: 0.3378 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 29377 Z= 0.323 Angle : 0.571 10.813 40452 Z= 0.305 Chirality : 0.042 0.162 4670 Planarity : 0.005 0.075 4894 Dihedral : 14.955 179.670 5430 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.33 % Favored : 93.61 % Rotamer: Outliers : 1.27 % Allowed : 10.05 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3505 helix: 1.24 (0.15), residues: 1246 sheet: -0.47 (0.20), residues: 636 loop : -1.28 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 293 HIS 0.006 0.001 HIS C 139 PHE 0.025 0.002 PHE A 166 TYR 0.016 0.002 TYR A 320 ARG 0.004 0.001 ARG A1090 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10885.92 seconds wall clock time: 271 minutes 11.13 seconds (16271.13 seconds total)