Starting phenix.real_space_refine on Tue Nov 19 17:15:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7v_18234/11_2024/8q7v_18234_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7v_18234/11_2024/8q7v_18234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7v_18234/11_2024/8q7v_18234.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7v_18234/11_2024/8q7v_18234.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7v_18234/11_2024/8q7v_18234_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q7v_18234/11_2024/8q7v_18234_trim.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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 106 5.16 5 C 17381 2.51 5 N 4958 2.21 5 O 5502 1.98 5 H 24559 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 170 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: 52613 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': 2, 'PTRANS': 91, '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: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 899 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} 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: 22.73, per 1000 atoms: 0.43 Number of scatterers: 52613 At special positions: 0 Unit cell: (135.16, 162.44, 215.76, 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 106 16.00 P 106 15.00 Mg 1 11.99 O 5502 8.00 N 4958 7.00 C 17381 6.00 H 24559 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: 13.12 Conformation dependent library (CDL) restraints added in 5.7 seconds 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6594 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 30 sheets defined 36.9% alpha, 19.7% beta 32 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 21.43 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 1424 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: 3.616A pdb=" N PHE C 718 " --> pdb=" O LEU C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 731 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: 4.059A 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: 3.586A pdb=" N TRP C 772 " --> pdb=" O GLN C 768 " (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 '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: 6.983A pdb=" N THR C 686 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN C 743 " --> pdb=" O PHE C 735 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N PHE C 735 " --> pdb=" O ASN C 743 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU C 745 " --> pdb=" O TRP C 733 " (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) 1165 hydrogen bonds defined for protein. 3309 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: 25.74 Time building geometry restraints manager: 15.76 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: 24522 1.13 - 1.30: 4505 1.30 - 1.47: 11959 1.47 - 1.64: 12247 1.64 - 1.81: 175 Bond restraints: 53408 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 53403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.19: 89437 4.19 - 8.37: 6479 8.37 - 12.56: 52 12.56 - 16.74: 4 16.74 - 20.93: 2 Bond angle restraints: 95974 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=" C ASN C 710 " pdb=" N ARG C 711 " pdb=" CA ARG C 711 " ideal model delta sigma weight residual 121.54 133.58 -12.04 1.91e+00 2.74e-01 3.97e+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 ... (remaining 95969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 24624 35.47 - 70.94: 998 70.94 - 106.41: 71 106.41 - 141.88: 5 141.88 - 177.35: 6 Dihedral angle restraints: 25704 sinusoidal: 13940 harmonic: 11764 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 25701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 4235 0.097 - 0.195: 327 0.195 - 0.292: 22 0.292 - 0.390: 3 0.390 - 0.487: 1 Chirality restraints: 4588 Sorted by residual: chirality pdb=" CA LYS C 763 " pdb=" N LYS C 763 " pdb=" C LYS C 763 " pdb=" CB LYS C 763 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.94e+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 4585 not shown) Planarity restraints: 8158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1275 " 0.280 9.50e-02 1.11e+02 1.39e-01 2.50e+02 pdb=" NE ARG A1275 " -0.097 2.00e-02 2.50e+03 pdb=" CZ ARG A1275 " -0.080 2.00e-02 2.50e+03 pdb=" NH1 ARG A1275 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A1275 " -0.090 2.00e-02 2.50e+03 pdb="HH11 ARG A1275 " 0.106 2.00e-02 2.50e+03 pdb="HH12 ARG A1275 " 0.037 2.00e-02 2.50e+03 pdb="HH21 ARG A1275 " 0.226 2.00e-02 2.50e+03 pdb="HH22 ARG A1275 " -0.090 2.00e-02 2.50e+03 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 ... (remaining 8155 not shown) Histogram of nonbonded interaction distances: 1.32 - 1.98: 1273 1.98 - 2.63: 57168 2.63 - 3.29: 144338 3.29 - 3.94: 188998 3.94 - 4.60: 283917 Nonbonded interactions: 675694 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 675689 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.240 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: 0.870 Extract box with map and model: 1.890 Check model and map are aligned: 0.380 Set scattering table: 0.430 Process input model: 122.930 Find NCS groups from input model: 0.560 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 28849 Z= 0.297 Angle : 0.931 14.426 39746 Z= 0.553 Chirality : 0.054 0.487 4588 Planarity : 0.008 0.146 4801 Dihedral : 13.731 177.352 10783 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.10 % Favored : 95.76 % Rotamer: Outliers : 0.13 % Allowed : 1.51 % Favored : 98.36 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.13 % 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: 3440 helix: -2.33 (0.11), residues: 1125 sheet: -0.89 (0.20), residues: 611 loop : -2.03 (0.13), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.005 TRP C 724 HIS 0.013 0.001 HIS A1460 PHE 0.092 0.003 PHE A1423 TYR 0.052 0.002 TYR A1389 ARG 0.008 0.001 ARG A1275 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 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 384 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 381 time to evaluate : 4.180 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 271 MET cc_start: 0.7153 (mtm) cc_final: 0.6872 (mtp) REVERT: A 992 LEU cc_start: 0.9429 (tp) cc_final: 0.9221 (tp) REVERT: A 1234 ASP cc_start: 0.9203 (m-30) cc_final: 0.8946 (t70) REVERT: A 1238 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8697 (tp-100) REVERT: A 1652 MET cc_start: 0.3725 (mtt) cc_final: 0.3318 (mtm) REVERT: B 63 MET cc_start: 0.6163 (mtm) cc_final: 0.5147 (tmm) REVERT: C 203 MET cc_start: 0.8519 (tpp) cc_final: 0.8271 (tpp) REVERT: C 392 LEU cc_start: 0.7909 (tp) cc_final: 0.7593 (tt) REVERT: C 759 LEU cc_start: 0.8967 (tp) cc_final: 0.8614 (mp) REVERT: G 78 THR cc_start: 0.5481 (p) cc_final: 0.5207 (p) REVERT: G 92 LEU cc_start: 0.8629 (mt) cc_final: 0.8288 (mt) REVERT: d 76 MET cc_start: 0.8286 (pp-130) cc_final: 0.8054 (ppp) outliers start: 3 outliers final: 0 residues processed: 384 average time/residue: 0.9645 time to fit residues: 566.2964 Evaluate side-chains 222 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 4.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 298 optimal weight: 10.0000 chunk 267 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 180 optimal weight: 0.8980 chunk 142 optimal weight: 7.9990 chunk 276 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 205 optimal weight: 0.9980 chunk 320 optimal weight: 9.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 112 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 ASN A1023 ASN A1367 ASN A1451 ASN ** A1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1712 HIS C 154 HIS C 201 ASN C 245 HIS C 280 HIS ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 ASN C 642 HIS d 16 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 28849 Z= 0.378 Angle : 0.696 8.573 39746 Z= 0.383 Chirality : 0.045 0.182 4588 Planarity : 0.006 0.087 4801 Dihedral : 15.821 179.366 5353 Min Nonbonded Distance : 1.521 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.69 % Favored : 96.16 % Rotamer: Outliers : 1.13 % Allowed : 5.49 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -1.38 (0.13), residues: 3440 helix: -0.14 (0.14), residues: 1173 sheet: -0.73 (0.19), residues: 651 loop : -1.55 (0.14), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 531 HIS 0.011 0.002 HIS C 437 PHE 0.020 0.002 PHE C 717 TYR 0.026 0.002 TYR A 431 ARG 0.011 0.001 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 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 240 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 213 time to evaluate : 4.190 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 147 MET cc_start: 0.8100 (mmp) cc_final: 0.7718 (mmp) REVERT: A 1238 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8653 (tp-100) REVERT: A 1389 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.7447 (t80) REVERT: A 1652 MET cc_start: 0.4003 (mtt) cc_final: 0.3548 (mtm) REVERT: B 63 MET cc_start: 0.6395 (mtm) cc_final: 0.5497 (tmm) REVERT: C 123 MET cc_start: 0.8702 (mtm) cc_final: 0.8488 (mtm) REVERT: C 392 LEU cc_start: 0.8398 (tp) cc_final: 0.8198 (tt) REVERT: C 433 MET cc_start: 0.8401 (ttp) cc_final: 0.8041 (ttp) REVERT: C 627 HIS cc_start: 0.7066 (OUTLIER) cc_final: 0.6837 (t-90) REVERT: C 759 LEU cc_start: 0.9142 (tp) cc_final: 0.8843 (mp) outliers start: 27 outliers final: 18 residues processed: 234 average time/residue: 0.9246 time to fit residues: 337.8220 Evaluate side-chains 205 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 4.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1181 ASP Chi-restraints excluded: chain A residue 1263 TRP Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1389 TYR Chi-restraints excluded: chain A residue 1442 PHE Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 627 HIS Chi-restraints excluded: chain C residue 866 SER Chi-restraints excluded: chain C residue 897 SER Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain d residue 41 CYS Chi-restraints excluded: chain d residue 71 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 178 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 266 optimal weight: 50.0000 chunk 218 optimal weight: 0.7980 chunk 88 optimal weight: 8.9990 chunk 321 optimal weight: 50.0000 chunk 346 optimal weight: 0.1980 chunk 286 optimal weight: 50.0000 chunk 318 optimal weight: 50.0000 chunk 109 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 333 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 ASN A1296 GLN A1367 ASN A1460 HIS ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28849 Z= 0.169 Angle : 0.524 7.075 39746 Z= 0.281 Chirality : 0.041 0.182 4588 Planarity : 0.004 0.070 4801 Dihedral : 15.578 178.729 5353 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.97 % Favored : 96.98 % Rotamer: Outliers : 0.92 % Allowed : 6.25 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -0.68 (0.14), residues: 3440 helix: 0.67 (0.15), residues: 1188 sheet: -0.60 (0.19), residues: 645 loop : -1.20 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1263 HIS 0.006 0.001 HIS C 802 PHE 0.017 0.001 PHE A 166 TYR 0.017 0.001 TYR A 431 ARG 0.006 0.001 ARG C 711 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 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 212 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 4.009 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: A 599 MET cc_start: 0.6818 (mmm) cc_final: 0.6585 (mmm) REVERT: A 1238 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8737 (tp-100) REVERT: A 1652 MET cc_start: 0.3951 (mtt) cc_final: 0.3478 (mtm) REVERT: B 63 MET cc_start: 0.6340 (mtm) cc_final: 0.5351 (tmm) REVERT: C 123 MET cc_start: 0.8787 (mtm) cc_final: 0.8513 (mtm) REVERT: C 759 LEU cc_start: 0.9100 (tp) cc_final: 0.8808 (mp) REVERT: C 822 MET cc_start: 0.7411 (tpp) cc_final: 0.7195 (tpp) REVERT: d 29 ARG cc_start: 0.7725 (tpp-160) cc_final: 0.7434 (tpp-160) REVERT: d 39 MET cc_start: 0.5389 (mpp) cc_final: 0.5010 (mmm) outliers start: 22 outliers final: 19 residues processed: 204 average time/residue: 0.9512 time to fit residues: 308.5906 Evaluate side-chains 202 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 4.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 1181 ASP Chi-restraints excluded: chain A residue 1353 PHE Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1442 PHE Chi-restraints excluded: chain A residue 1534 PHE Chi-restraints excluded: chain A residue 1644 LEU Chi-restraints excluded: chain A residue 1741 TYR Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 866 SER Chi-restraints excluded: chain C residue 897 SER Chi-restraints excluded: chain d residue 71 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 317 optimal weight: 10.0000 chunk 241 optimal weight: 6.9990 chunk 166 optimal weight: 0.0980 chunk 35 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 322 optimal weight: 3.9990 chunk 341 optimal weight: 30.0000 chunk 168 optimal weight: 9.9990 chunk 305 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 357 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN ** A1227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1352 HIS C 802 HIS H 81 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 28849 Z= 0.370 Angle : 0.648 7.977 39746 Z= 0.352 Chirality : 0.044 0.402 4588 Planarity : 0.005 0.073 4801 Dihedral : 15.663 173.770 5353 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.29 % Favored : 94.68 % Rotamer: Outliers : 1.43 % Allowed : 6.29 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -0.90 (0.14), residues: 3440 helix: 0.50 (0.15), residues: 1182 sheet: -0.71 (0.20), residues: 651 loop : -1.35 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1263 HIS 0.013 0.002 HIS C 139 PHE 0.021 0.002 PHE C 339 TYR 0.017 0.002 TYR A 614 ARG 0.006 0.001 ARG C 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 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 209 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 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: A 164 MET cc_start: 0.8883 (ttp) cc_final: 0.8665 (ttp) REVERT: A 259 ASP cc_start: 0.8195 (t0) cc_final: 0.7942 (p0) REVERT: A 613 TYR cc_start: 0.7900 (m-80) cc_final: 0.7572 (m-10) REVERT: A 1095 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8930 (pt) REVERT: A 1223 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7508 (pp20) REVERT: A 1238 GLN cc_start: 0.9220 (mm-40) cc_final: 0.8821 (tp-100) REVERT: A 1249 MET cc_start: 0.7877 (mmp) cc_final: 0.6823 (mmm) REVERT: A 1389 TYR cc_start: 0.7747 (OUTLIER) cc_final: 0.7342 (t80) REVERT: A 1652 MET cc_start: 0.4016 (mtt) cc_final: 0.3565 (mtm) REVERT: B 63 MET cc_start: 0.6296 (mtm) cc_final: 0.5738 (tmm) REVERT: C 123 MET cc_start: 0.8920 (mtm) cc_final: 0.8651 (mtm) REVERT: C 389 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7691 (m-30) REVERT: C 627 HIS cc_start: 0.6282 (OUTLIER) cc_final: 0.5828 (t-90) REVERT: C 759 LEU cc_start: 0.9147 (tp) cc_final: 0.8892 (mp) REVERT: C 914 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7547 (mmtt) REVERT: d 39 MET cc_start: 0.5749 (mpp) cc_final: 0.5500 (mmm) outliers start: 34 outliers final: 20 residues processed: 197 average time/residue: 0.8426 time to fit residues: 268.0059 Evaluate side-chains 188 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 4.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1181 ASP Chi-restraints excluded: chain A residue 1223 GLU Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1389 TYR Chi-restraints excluded: chain A residue 1442 PHE Chi-restraints excluded: chain A residue 1534 PHE Chi-restraints excluded: chain A residue 1741 TYR Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 627 HIS Chi-restraints excluded: chain C residue 866 SER Chi-restraints excluded: chain C residue 897 SER Chi-restraints excluded: chain d residue 71 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 284 optimal weight: 40.0000 chunk 193 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 254 optimal weight: 0.7980 chunk 140 optimal weight: 10.0000 chunk 291 optimal weight: 20.0000 chunk 235 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 174 optimal weight: 10.0000 chunk 306 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 overall best weight: 6.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1069 ASN A1227 GLN A1367 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 28849 Z= 0.483 Angle : 0.734 8.371 39746 Z= 0.400 Chirality : 0.046 0.170 4588 Planarity : 0.006 0.079 4801 Dihedral : 15.931 171.988 5353 Min Nonbonded Distance : 1.505 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.12 % Favored : 92.85 % Rotamer: Outliers : 1.59 % Allowed : 7.42 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -1.76 (0.14), residues: 3440 helix: -0.22 (0.14), residues: 1181 sheet: -1.14 (0.20), residues: 625 loop : -1.87 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A1263 HIS 0.019 0.003 HIS C 139 PHE 0.037 0.003 PHE C 369 TYR 0.024 0.003 TYR C 161 ARG 0.011 0.001 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 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 205 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 4.150 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: A 164 MET cc_start: 0.9027 (ttp) cc_final: 0.8725 (ttp) REVERT: A 423 ASP cc_start: 0.9034 (OUTLIER) cc_final: 0.8415 (t0) REVERT: A 599 MET cc_start: 0.7158 (mmm) cc_final: 0.6850 (mmt) REVERT: A 613 TYR cc_start: 0.8008 (m-80) cc_final: 0.7790 (m-10) REVERT: A 1237 MET cc_start: 0.8857 (mtm) cc_final: 0.8610 (mtp) REVERT: A 1238 GLN cc_start: 0.9303 (mm-40) cc_final: 0.8981 (tp-100) REVERT: A 1249 MET cc_start: 0.8107 (mmp) cc_final: 0.6944 (mmm) REVERT: A 1307 MET cc_start: 0.8388 (ttp) cc_final: 0.8159 (tpp) REVERT: A 1389 TYR cc_start: 0.7870 (OUTLIER) cc_final: 0.7363 (t80) REVERT: A 1652 MET cc_start: 0.3478 (mtt) cc_final: 0.3159 (mtm) REVERT: C 759 LEU cc_start: 0.9106 (tp) cc_final: 0.8817 (mp) REVERT: C 822 MET cc_start: 0.7779 (tpp) cc_final: 0.7545 (tpp) outliers start: 38 outliers final: 28 residues processed: 198 average time/residue: 0.8595 time to fit residues: 275.7810 Evaluate side-chains 180 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 4.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 1181 ASP Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1389 TYR Chi-restraints excluded: chain A residue 1442 PHE Chi-restraints excluded: chain A residue 1534 PHE Chi-restraints excluded: chain A residue 1636 LYS Chi-restraints excluded: chain A residue 1644 LEU Chi-restraints excluded: chain A residue 1741 TYR Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 497 LEU Chi-restraints excluded: chain C residue 627 HIS Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 866 SER Chi-restraints excluded: chain C residue 912 LEU Chi-restraints excluded: chain d residue 71 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 114 optimal weight: 4.9990 chunk 307 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 200 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 341 optimal weight: 30.0000 chunk 283 optimal weight: 50.0000 chunk 158 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1367 ASN ** C 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.6577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28849 Z= 0.212 Angle : 0.557 6.787 39746 Z= 0.297 Chirality : 0.041 0.168 4588 Planarity : 0.005 0.145 4801 Dihedral : 15.585 174.494 5353 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.38 % Rotamer: Outliers : 1.30 % Allowed : 8.22 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -1.09 (0.14), residues: 3440 helix: 0.55 (0.15), residues: 1194 sheet: -0.98 (0.20), residues: 628 loop : -1.59 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A1263 HIS 0.005 0.001 HIS C 491 PHE 0.015 0.001 PHE H 80 TYR 0.014 0.001 TYR A 564 ARG 0.012 0.000 ARG C 813 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 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 187 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 4.128 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: A 599 MET cc_start: 0.7023 (mmm) cc_final: 0.6737 (mmt) REVERT: A 613 TYR cc_start: 0.7812 (m-80) cc_final: 0.7517 (m-10) REVERT: A 1237 MET cc_start: 0.8811 (mtm) cc_final: 0.8600 (mtp) REVERT: A 1238 GLN cc_start: 0.9271 (mm-40) cc_final: 0.8971 (tp-100) REVERT: A 1249 MET cc_start: 0.8102 (mmp) cc_final: 0.6962 (mmm) REVERT: A 1307 MET cc_start: 0.8489 (ttp) cc_final: 0.8208 (tpp) REVERT: A 1389 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.7295 (t80) REVERT: A 1652 MET cc_start: 0.3535 (mtt) cc_final: 0.3154 (mtm) REVERT: C 627 HIS cc_start: 0.6999 (OUTLIER) cc_final: 0.6424 (t-90) REVERT: C 759 LEU cc_start: 0.9111 (tp) cc_final: 0.8895 (mm) REVERT: C 822 MET cc_start: 0.7644 (tpp) cc_final: 0.7304 (tpp) outliers start: 31 outliers final: 24 residues processed: 180 average time/residue: 0.8528 time to fit residues: 248.4846 Evaluate side-chains 177 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 4.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1181 ASP Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1389 TYR Chi-restraints excluded: chain A residue 1534 PHE Chi-restraints excluded: chain A residue 1644 LEU Chi-restraints excluded: chain A residue 1741 TYR Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 627 HIS Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 813 ARG Chi-restraints excluded: chain C residue 866 SER Chi-restraints excluded: chain d residue 71 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 329 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 193 optimal weight: 0.6980 chunk 287 optimal weight: 7.9990 chunk 190 optimal weight: 0.6980 chunk 340 optimal weight: 6.9990 chunk 212 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 157 optimal weight: 20.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN A1367 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.6713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28849 Z= 0.183 Angle : 0.524 8.782 39746 Z= 0.277 Chirality : 0.041 0.231 4588 Planarity : 0.004 0.068 4801 Dihedral : 15.309 175.582 5353 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.12 % Favored : 94.85 % Rotamer: Outliers : 1.22 % Allowed : 8.34 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -0.69 (0.14), residues: 3440 helix: 1.00 (0.15), residues: 1197 sheet: -0.94 (0.20), residues: 646 loop : -1.37 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.001 TRP A1263 HIS 0.005 0.001 HIS H 81 PHE 0.019 0.001 PHE H 80 TYR 0.013 0.001 TYR A 431 ARG 0.005 0.000 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 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 183 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 4.132 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: A 599 MET cc_start: 0.7079 (mmm) cc_final: 0.6804 (mmt) REVERT: A 613 TYR cc_start: 0.7783 (m-80) cc_final: 0.7466 (m-10) REVERT: A 1013 ASN cc_start: 0.8868 (m-40) cc_final: 0.8621 (m110) REVERT: A 1237 MET cc_start: 0.8849 (mtm) cc_final: 0.8635 (mtp) REVERT: A 1238 GLN cc_start: 0.9261 (mm-40) cc_final: 0.8944 (tp-100) REVERT: A 1249 MET cc_start: 0.8163 (mmp) cc_final: 0.6966 (mmm) REVERT: A 1307 MET cc_start: 0.8498 (ttp) cc_final: 0.8221 (tpp) REVERT: A 1389 TYR cc_start: 0.7806 (OUTLIER) cc_final: 0.7268 (t80) REVERT: A 1652 MET cc_start: 0.3628 (mtt) cc_final: 0.3257 (mtm) REVERT: C 627 HIS cc_start: 0.6797 (OUTLIER) cc_final: 0.6358 (t-90) REVERT: C 759 LEU cc_start: 0.9140 (tp) cc_final: 0.8903 (mm) outliers start: 29 outliers final: 21 residues processed: 174 average time/residue: 0.8841 time to fit residues: 251.7256 Evaluate side-chains 175 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 3.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1181 ASP Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1389 TYR Chi-restraints excluded: chain A residue 1534 PHE Chi-restraints excluded: chain A residue 1644 LEU Chi-restraints excluded: chain A residue 1741 TYR Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 627 HIS Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 866 SER Chi-restraints excluded: chain d residue 71 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 210 optimal weight: 0.5980 chunk 135 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 216 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 267 optimal weight: 50.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1367 ASN ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.6821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28849 Z= 0.168 Angle : 0.507 6.894 39746 Z= 0.268 Chirality : 0.040 0.165 4588 Planarity : 0.004 0.067 4801 Dihedral : 15.169 176.169 5353 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.45 % Favored : 95.52 % Rotamer: Outliers : 1.05 % Allowed : 8.60 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -0.47 (0.15), residues: 3440 helix: 1.28 (0.15), residues: 1196 sheet: -0.90 (0.20), residues: 668 loop : -1.28 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP A1263 HIS 0.006 0.001 HIS A 755 PHE 0.019 0.001 PHE H 80 TYR 0.011 0.001 TYR A 431 ARG 0.005 0.000 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 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 182 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 3.991 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: A 423 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8341 (t0) REVERT: A 599 MET cc_start: 0.7143 (mmm) cc_final: 0.6877 (mmt) REVERT: A 1013 ASN cc_start: 0.8829 (m-40) cc_final: 0.8581 (m110) REVERT: A 1095 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8726 (pt) REVERT: A 1237 MET cc_start: 0.8861 (mtm) cc_final: 0.8645 (mtp) REVERT: A 1238 GLN cc_start: 0.9318 (mm-40) cc_final: 0.8995 (tp-100) REVERT: A 1249 MET cc_start: 0.8227 (mmp) cc_final: 0.7076 (mmm) REVERT: A 1307 MET cc_start: 0.8545 (ttp) cc_final: 0.8272 (tpp) REVERT: A 1389 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.7139 (t80) REVERT: A 1652 MET cc_start: 0.3598 (mtt) cc_final: 0.3226 (mtm) REVERT: C 627 HIS cc_start: 0.6774 (OUTLIER) cc_final: 0.6237 (t-90) REVERT: C 822 MET cc_start: 0.7632 (tpp) cc_final: 0.7399 (tpp) outliers start: 25 outliers final: 16 residues processed: 178 average time/residue: 0.8462 time to fit residues: 247.9252 Evaluate side-chains 171 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 4.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1181 ASP Chi-restraints excluded: chain A residue 1389 TYR Chi-restraints excluded: chain A residue 1534 PHE Chi-restraints excluded: chain A residue 1644 LEU Chi-restraints excluded: chain A residue 1741 TYR Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 627 HIS Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 866 SER Chi-restraints excluded: chain d residue 71 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 309 optimal weight: 9.9990 chunk 325 optimal weight: 7.9990 chunk 297 optimal weight: 6.9990 chunk 317 optimal weight: 9.9990 chunk 190 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 286 optimal weight: 0.0270 chunk 299 optimal weight: 7.9990 chunk 315 optimal weight: 50.0000 overall best weight: 2.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.7039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28849 Z= 0.201 Angle : 0.517 6.651 39746 Z= 0.274 Chirality : 0.040 0.170 4588 Planarity : 0.004 0.067 4801 Dihedral : 15.122 175.805 5353 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.67 % Favored : 94.30 % Rotamer: Outliers : 0.92 % Allowed : 8.64 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -0.44 (0.15), residues: 3440 helix: 1.31 (0.15), residues: 1197 sheet: -0.77 (0.21), residues: 630 loop : -1.32 (0.16), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A1263 HIS 0.005 0.001 HIS C 477 PHE 0.019 0.001 PHE H 80 TYR 0.014 0.001 TYR A1369 ARG 0.006 0.000 ARG H 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 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 174 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 4.066 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: A 259 ASP cc_start: 0.8185 (t0) cc_final: 0.7982 (p0) REVERT: A 423 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8321 (t0) REVERT: A 599 MET cc_start: 0.7166 (mmm) cc_final: 0.6886 (mmt) REVERT: A 613 TYR cc_start: 0.7932 (m-80) cc_final: 0.7599 (m-10) REVERT: A 1013 ASN cc_start: 0.8735 (m-40) cc_final: 0.8484 (m110) REVERT: A 1095 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8737 (pt) REVERT: A 1237 MET cc_start: 0.8842 (mtm) cc_final: 0.8618 (mtp) REVERT: A 1238 GLN cc_start: 0.9276 (mm-40) cc_final: 0.8986 (tp-100) REVERT: A 1249 MET cc_start: 0.8220 (mmp) cc_final: 0.6823 (mmm) REVERT: A 1307 MET cc_start: 0.8574 (ttp) cc_final: 0.8288 (tpp) REVERT: A 1389 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.7138 (t80) REVERT: A 1652 MET cc_start: 0.3693 (mtt) cc_final: 0.3329 (mtm) REVERT: C 627 HIS cc_start: 0.6769 (OUTLIER) cc_final: 0.6310 (t-90) outliers start: 22 outliers final: 16 residues processed: 171 average time/residue: 0.8120 time to fit residues: 227.3572 Evaluate side-chains 171 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 4.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1181 ASP Chi-restraints excluded: chain A residue 1389 TYR Chi-restraints excluded: chain A residue 1534 PHE Chi-restraints excluded: chain A residue 1644 LEU Chi-restraints excluded: chain A residue 1741 TYR Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 627 HIS Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 866 SER Chi-restraints excluded: chain d residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 208 optimal weight: 0.9980 chunk 335 optimal weight: 50.0000 chunk 204 optimal weight: 0.0980 chunk 159 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 351 optimal weight: 50.0000 chunk 323 optimal weight: 50.0000 chunk 280 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.7117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28849 Z= 0.163 Angle : 0.503 6.877 39746 Z= 0.264 Chirality : 0.040 0.170 4588 Planarity : 0.004 0.066 4801 Dihedral : 15.032 177.027 5353 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.51 % Favored : 95.47 % Rotamer: Outliers : 0.84 % Allowed : 8.68 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -0.28 (0.15), residues: 3440 helix: 1.49 (0.16), residues: 1202 sheet: -0.72 (0.21), residues: 635 loop : -1.26 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1263 HIS 0.005 0.001 HIS A 755 PHE 0.021 0.001 PHE H 80 TYR 0.011 0.001 TYR A 431 ARG 0.007 0.000 ARG H 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6880 Ramachandran restraints generated. 3440 Oldfield, 0 Emsley, 3440 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 174 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 4.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8329 (t0) REVERT: A 599 MET cc_start: 0.7157 (mmm) cc_final: 0.6876 (mmt) REVERT: A 899 MET cc_start: 0.7646 (ttm) cc_final: 0.7365 (tmm) REVERT: A 1013 ASN cc_start: 0.8689 (m-40) cc_final: 0.8424 (m110) REVERT: A 1095 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8726 (pt) REVERT: A 1237 MET cc_start: 0.8835 (mtm) cc_final: 0.8614 (mtp) REVERT: A 1238 GLN cc_start: 0.9253 (mm-40) cc_final: 0.9006 (tp-100) REVERT: A 1249 MET cc_start: 0.8224 (mmp) cc_final: 0.6876 (mmm) REVERT: A 1307 MET cc_start: 0.8561 (ttp) cc_final: 0.8291 (tpp) REVERT: A 1389 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.7120 (t80) REVERT: A 1652 MET cc_start: 0.3656 (mtt) cc_final: 0.3386 (mtm) REVERT: C 627 HIS cc_start: 0.6731 (OUTLIER) cc_final: 0.6263 (t-90) REVERT: C 822 MET cc_start: 0.7578 (tpp) cc_final: 0.7338 (tpp) outliers start: 20 outliers final: 16 residues processed: 172 average time/residue: 0.8300 time to fit residues: 233.7000 Evaluate side-chains 171 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 3.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 505 ASN Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1097 ILE Chi-restraints excluded: chain A residue 1181 ASP Chi-restraints excluded: chain A residue 1389 TYR Chi-restraints excluded: chain A residue 1534 PHE Chi-restraints excluded: chain A residue 1644 LEU Chi-restraints excluded: chain A residue 1741 TYR Chi-restraints excluded: chain A residue 1743 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 486 ASP Chi-restraints excluded: chain C residue 627 HIS Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 866 SER Chi-restraints excluded: chain d residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 222 optimal weight: 4.9990 chunk 298 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 chunk 258 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 280 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 288 optimal weight: 50.0000 chunk 35 optimal weight: 0.2980 chunk 51 optimal weight: 5.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 ASN A1035 GLN G 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.084336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.061614 restraints weight = 450835.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.063307 restraints weight = 198909.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.064368 restraints weight = 120656.800| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.7493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 28849 Z= 0.319 Angle : 0.583 7.975 39746 Z= 0.313 Chirality : 0.042 0.180 4588 Planarity : 0.005 0.067 4801 Dihedral : 15.228 175.317 5353 Min Nonbonded Distance : 1.649 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.09 % Favored : 92.88 % Rotamer: Outliers : 0.96 % Allowed : 8.72 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -0.67 (0.14), residues: 3440 helix: 1.08 (0.15), residues: 1193 sheet: -0.81 (0.21), residues: 617 loop : -1.45 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1263 HIS 0.007 0.001 HIS C 903 PHE 0.020 0.002 PHE C 200 TYR 0.017 0.002 TYR A 520 ARG 0.007 0.001 ARG H 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9124.38 seconds wall clock time: 215 minutes 59.38 seconds (12959.38 seconds total)