Starting phenix.real_space_refine on Fri Sep 27 22:21:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woo_32653/09_2024/7woo_32653_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woo_32653/09_2024/7woo_32653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woo_32653/09_2024/7woo_32653.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woo_32653/09_2024/7woo_32653.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woo_32653/09_2024/7woo_32653_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7woo_32653/09_2024/7woo_32653_neut.cif" } resolution = 3.71 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= 0.008 sd= 0.043 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: 4 Type Number sf(0) Gaussians S 166 5.16 5 C 42652 2.51 5 N 11167 2.21 5 O 12964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 292 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 66949 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5723 Classifications: {'peptide': 732} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 17, 'TRANS': 714} Chain breaks: 4 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 113 Chain: "C" Number of atoms: 10452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1325, 10452 Classifications: {'peptide': 1325} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 46, 'TRANS': 1275} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 10976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1398, 10976 Classifications: {'peptide': 1398} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'CIS': 3, 'PTRANS': 49, 'TRANS': 1345} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 108 Chain: "E" Number of atoms: 12362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1552, 12362 Classifications: {'peptide': 1552} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 43, 'TRANS': 1508} Chain breaks: 6 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 92 Chain: "F" Number of atoms: 12232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1622, 12232 Classifications: {'peptide': 1622} Incomplete info: {'truncation_to_alanine': 218} Link IDs: {'PTRANS': 38, 'TRANS': 1583} Chain breaks: 2 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 832 Unresolved non-hydrogen angles: 1070 Unresolved non-hydrogen dihedrals: 711 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 2, 'TYR:plan': 19, 'ASN:plan1': 16, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 12, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 446 Chain: "G" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1533 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 195} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "H" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1811 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 7, 'TRANS': 238} Chain breaks: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Chain: "I" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1418 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 186} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "J" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1492 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 190} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "K" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1808 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 7, 'TRANS': 246} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 123 Chain: "L" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1366 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'TRANS': 186} Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 5, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "Z" Number of atoms: 5776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5776 Classifications: {'peptide': 746} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 17, 'TRANS': 728} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 337 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 167 Time building chain proxies: 28.61, per 1000 atoms: 0.43 Number of scatterers: 66949 At special positions: 0 Unit cell: (264.528, 323.312, 257.848, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 166 16.00 O 12964 8.00 N 11167 7.00 C 42652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.83 Conformation dependent library (CDL) restraints added in 6.8 seconds 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16676 Finding SS restraints... Secondary structure from input PDB file: 374 helices and 26 sheets defined 62.1% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.72 Creating SS restraints... Processing helix chain 'A' and resid 13 through 31 removed outlier: 3.708A pdb=" N LEU A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 80 through 92 Processing helix chain 'A' and resid 113 through 140 removed outlier: 3.978A pdb=" N ASP A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 Processing helix chain 'A' and resid 201 through 204 Processing helix chain 'A' and resid 205 through 228 Processing helix chain 'A' and resid 233 through 243 Processing helix chain 'A' and resid 248 through 263 Processing helix chain 'A' and resid 269 through 294 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 333 through 343 Processing helix chain 'A' and resid 345 through 356 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 377 removed outlier: 3.708A pdb=" N LEU A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 398 removed outlier: 3.569A pdb=" N LYS A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 431 through 442 Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 458 through 470 Processing helix chain 'A' and resid 477 through 485 Processing helix chain 'A' and resid 487 through 497 Processing helix chain 'A' and resid 499 through 513 Processing helix chain 'A' and resid 533 through 543 Processing helix chain 'A' and resid 549 through 559 removed outlier: 3.810A pdb=" N LEU A 559 " --> pdb=" O GLU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 Processing helix chain 'A' and resid 565 through 584 Processing helix chain 'A' and resid 585 through 590 Processing helix chain 'A' and resid 602 through 607 Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 615 through 635 removed outlier: 4.153A pdb=" N GLU A 625 " --> pdb=" O HIS A 621 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 647 Processing helix chain 'A' and resid 649 through 668 Processing helix chain 'A' and resid 684 through 697 Processing helix chain 'A' and resid 699 through 705 removed outlier: 3.732A pdb=" N GLN A 705 " --> pdb=" O GLY A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 729 Processing helix chain 'A' and resid 731 through 742 Processing helix chain 'A' and resid 749 through 763 removed outlier: 3.977A pdb=" N ALA A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG A 754 " --> pdb=" O GLU A 750 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN A 762 " --> pdb=" O GLN A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 769 Processing helix chain 'A' and resid 770 through 792 Processing helix chain 'A' and resid 796 through 820 removed outlier: 3.722A pdb=" N GLY A 800 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN A 801 " --> pdb=" O SER A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 824 Processing helix chain 'A' and resid 825 through 838 Processing helix chain 'C' and resid 68 through 72 removed outlier: 3.838A pdb=" N SER C 71 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 107 Processing helix chain 'C' and resid 113 through 118 removed outlier: 4.259A pdb=" N TYR C 117 " --> pdb=" O ASN C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 147 through 155 removed outlier: 3.567A pdb=" N GLN C 153 " --> pdb=" O GLU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 327 removed outlier: 4.076A pdb=" N LEU C 326 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE C 327 " --> pdb=" O GLY C 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 323 through 327' Processing helix chain 'C' and resid 380 through 391 Processing helix chain 'C' and resid 396 through 400 Processing helix chain 'C' and resid 456 through 462 removed outlier: 3.758A pdb=" N SER C 459 " --> pdb=" O THR C 456 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER C 461 " --> pdb=" O ILE C 458 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU C 462 " --> pdb=" O SER C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 514 through 518 removed outlier: 3.555A pdb=" N SER C 517 " --> pdb=" O ARG C 514 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY C 518 " --> pdb=" O ALA C 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 514 through 518' Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 588 through 593 Processing helix chain 'C' and resid 616 through 624 Processing helix chain 'C' and resid 628 through 636 Processing helix chain 'C' and resid 636 through 650 Processing helix chain 'C' and resid 654 through 668 Processing helix chain 'C' and resid 706 through 720 Processing helix chain 'C' and resid 748 through 774 Proline residue: C 771 - end of helix Processing helix chain 'C' and resid 786 through 816 Processing helix chain 'C' and resid 818 through 831 Processing helix chain 'C' and resid 837 through 847 Processing helix chain 'C' and resid 848 through 854 Processing helix chain 'C' and resid 856 through 877 Processing helix chain 'C' and resid 880 through 892 removed outlier: 3.797A pdb=" N ILE C 884 " --> pdb=" O SER C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 917 removed outlier: 3.513A pdb=" N ILE C 901 " --> pdb=" O HIS C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 938 Processing helix chain 'C' and resid 943 through 957 Processing helix chain 'C' and resid 959 through 975 Processing helix chain 'C' and resid 978 through 986 Processing helix chain 'C' and resid 994 through 1023 Processing helix chain 'C' and resid 1034 through 1049 Processing helix chain 'C' and resid 1052 through 1066 Processing helix chain 'C' and resid 1068 through 1073 Processing helix chain 'C' and resid 1079 through 1089 removed outlier: 4.138A pdb=" N GLU C1089 " --> pdb=" O LYS C1085 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1105 Processing helix chain 'C' and resid 1107 through 1121 Processing helix chain 'C' and resid 1126 through 1142 Processing helix chain 'C' and resid 1146 through 1148 No H-bonds generated for 'chain 'C' and resid 1146 through 1148' Processing helix chain 'C' and resid 1149 through 1179 removed outlier: 3.533A pdb=" N ASN C1179 " --> pdb=" O ASN C1175 " (cutoff:3.500A) Processing helix chain 'C' and resid 1184 through 1196 Processing helix chain 'C' and resid 1201 through 1209 removed outlier: 3.571A pdb=" N CYS C1209 " --> pdb=" O LEU C1205 " (cutoff:3.500A) Processing helix chain 'C' and resid 1215 through 1226 Processing helix chain 'C' and resid 1230 through 1248 Processing helix chain 'C' and resid 1256 through 1277 removed outlier: 3.950A pdb=" N SER C1260 " --> pdb=" O VAL C1256 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE C1261 " --> pdb=" O GLY C1257 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR C1275 " --> pdb=" O ARG C1271 " (cutoff:3.500A) Processing helix chain 'C' and resid 1284 through 1296 Processing helix chain 'C' and resid 1305 through 1314 removed outlier: 3.972A pdb=" N MET C1310 " --> pdb=" O SER C1306 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE C1311 " --> pdb=" O VAL C1307 " (cutoff:3.500A) Processing helix chain 'C' and resid 1317 through 1332 Processing helix chain 'C' and resid 1335 through 1354 Processing helix chain 'C' and resid 1354 through 1361 Processing helix chain 'C' and resid 1362 through 1368 removed outlier: 3.691A pdb=" N ILE C1366 " --> pdb=" O ALA C1362 " (cutoff:3.500A) Processing helix chain 'C' and resid 1373 through 1377 removed outlier: 3.817A pdb=" N ASP C1377 " --> pdb=" O PRO C1374 " (cutoff:3.500A) Processing helix chain 'C' and resid 1379 through 1388 removed outlier: 3.678A pdb=" N HIS C1388 " --> pdb=" O LYS C1384 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 117 Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 157 through 164 Processing helix chain 'D' and resid 300 through 304 removed outlier: 3.881A pdb=" N TRP D 304 " --> pdb=" O SER D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 333 through 339 Processing helix chain 'D' and resid 394 through 403 removed outlier: 4.036A pdb=" N GLY D 403 " --> pdb=" O SER D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 482 removed outlier: 4.390A pdb=" N VAL D 476 " --> pdb=" O THR D 473 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN D 479 " --> pdb=" O VAL D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 499 removed outlier: 3.823A pdb=" N LEU D 499 " --> pdb=" O PHE D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 588 removed outlier: 3.634A pdb=" N THR D 588 " --> pdb=" O GLY D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 662 Processing helix chain 'D' and resid 669 through 688 removed outlier: 7.788A pdb=" N ALA D 675 " --> pdb=" O LEU D 671 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N ALA D 676 " --> pdb=" O ASN D 672 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU D 677 " --> pdb=" O TYR D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 705 Processing helix chain 'D' and resid 767 through 781 Processing helix chain 'D' and resid 781 through 786 removed outlier: 4.543A pdb=" N GLY D 786 " --> pdb=" O ARG D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 856 Processing helix chain 'D' and resid 857 through 860 Processing helix chain 'D' and resid 880 through 883 removed outlier: 3.646A pdb=" N GLU D 883 " --> pdb=" O LYS D 880 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 880 through 883' Processing helix chain 'D' and resid 884 through 915 removed outlier: 3.593A pdb=" N GLU D 915 " --> pdb=" O ASN D 911 " (cutoff:3.500A) Processing helix chain 'D' and resid 929 through 934 Processing helix chain 'D' and resid 940 through 945 Processing helix chain 'D' and resid 948 through 954 removed outlier: 3.619A pdb=" N LEU D 952 " --> pdb=" O ASP D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 972 removed outlier: 4.066A pdb=" N LEU D 962 " --> pdb=" O LYS D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 979 through 990 removed outlier: 3.559A pdb=" N LEU D 988 " --> pdb=" O THR D 984 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN D 989 " --> pdb=" O ALA D 985 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1017 Processing helix chain 'D' and resid 1020 through 1038 removed outlier: 3.503A pdb=" N ILE D1038 " --> pdb=" O LEU D1034 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1042 Processing helix chain 'D' and resid 1043 through 1056 Processing helix chain 'D' and resid 1059 through 1075 removed outlier: 3.678A pdb=" N ASP D1075 " --> pdb=" O ALA D1071 " (cutoff:3.500A) Processing helix chain 'D' and resid 1078 through 1086 removed outlier: 3.542A pdb=" N GLN D1082 " --> pdb=" O LYS D1078 " (cutoff:3.500A) Processing helix chain 'D' and resid 1094 through 1121 Processing helix chain 'D' and resid 1135 through 1152 removed outlier: 3.991A pdb=" N VAL D1139 " --> pdb=" O ASN D1135 " (cutoff:3.500A) Processing helix chain 'D' and resid 1154 through 1168 Processing helix chain 'D' and resid 1170 through 1176 Processing helix chain 'D' and resid 1181 through 1191 removed outlier: 4.269A pdb=" N GLY D1191 " --> pdb=" O MET D1187 " (cutoff:3.500A) Processing helix chain 'D' and resid 1193 through 1207 removed outlier: 3.661A pdb=" N ARG D1207 " --> pdb=" O TYR D1203 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 through 1223 Processing helix chain 'D' and resid 1228 through 1244 Processing helix chain 'D' and resid 1248 through 1250 No H-bonds generated for 'chain 'D' and resid 1248 through 1250' Processing helix chain 'D' and resid 1251 through 1282 Processing helix chain 'D' and resid 1286 through 1298 Processing helix chain 'D' and resid 1303 through 1310 Processing helix chain 'D' and resid 1317 through 1328 Processing helix chain 'D' and resid 1332 through 1351 removed outlier: 3.563A pdb=" N PHE D1351 " --> pdb=" O LEU D1347 " (cutoff:3.500A) Processing helix chain 'D' and resid 1356 through 1379 Processing helix chain 'D' and resid 1386 through 1402 Proline residue: D1392 - end of helix Processing helix chain 'D' and resid 1412 through 1420 removed outlier: 3.833A pdb=" N PHE D1416 " --> pdb=" O ILE D1412 " (cutoff:3.500A) Processing helix chain 'D' and resid 1422 through 1437 Processing helix chain 'D' and resid 1441 through 1459 Processing helix chain 'D' and resid 1459 through 1466 Processing helix chain 'D' and resid 1467 through 1473 Processing helix chain 'D' and resid 1478 through 1481 Processing helix chain 'D' and resid 1482 through 1492 Processing helix chain 'E' and resid 19 through 25 removed outlier: 3.773A pdb=" N ASN E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 47 removed outlier: 5.054A pdb=" N GLN E 39 " --> pdb=" O LYS E 35 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE E 40 " --> pdb=" O GLN E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 78 Processing helix chain 'E' and resid 86 through 92 removed outlier: 3.732A pdb=" N ALA E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 119 removed outlier: 3.659A pdb=" N GLU E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE E 101 " --> pdb=" O HIS E 97 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL E 113 " --> pdb=" O ARG E 109 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL E 118 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 131 removed outlier: 3.647A pdb=" N TYR E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 151 Processing helix chain 'E' and resid 153 through 162 removed outlier: 3.799A pdb=" N SER E 158 " --> pdb=" O ILE E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 199 Processing helix chain 'E' and resid 206 through 219 removed outlier: 4.525A pdb=" N GLN E 217 " --> pdb=" O PHE E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 229 Processing helix chain 'E' and resid 254 through 273 removed outlier: 3.570A pdb=" N ARG E 260 " --> pdb=" O THR E 256 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE E 261 " --> pdb=" O LEU E 257 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU E 273 " --> pdb=" O THR E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 294 through 308 Processing helix chain 'E' and resid 318 through 336 removed outlier: 4.041A pdb=" N GLN E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 356 Processing helix chain 'E' and resid 357 through 369 removed outlier: 3.567A pdb=" N LYS E 361 " --> pdb=" O ASP E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 387 removed outlier: 4.523A pdb=" N THR E 376 " --> pdb=" O ASP E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 405 Processing helix chain 'E' and resid 408 through 414 Processing helix chain 'E' and resid 418 through 426 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 449 through 456 Processing helix chain 'E' and resid 560 through 580 Processing helix chain 'E' and resid 584 through 603 removed outlier: 3.706A pdb=" N HIS E 588 " --> pdb=" O ASP E 584 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP E 603 " --> pdb=" O THR E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 618 Processing helix chain 'E' and resid 633 through 648 removed outlier: 3.681A pdb=" N VAL E 637 " --> pdb=" O SER E 633 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG E 648 " --> pdb=" O ILE E 644 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 665 removed outlier: 3.601A pdb=" N ILE E 654 " --> pdb=" O ASP E 650 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET E 663 " --> pdb=" O GLU E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 668 through 679 removed outlier: 4.133A pdb=" N VAL E 672 " --> pdb=" O TYR E 668 " (cutoff:3.500A) Processing helix chain 'E' and resid 707 through 723 removed outlier: 3.858A pdb=" N ARG E 720 " --> pdb=" O LYS E 716 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU E 721 " --> pdb=" O VAL E 717 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU E 723 " --> pdb=" O ILE E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 731 through 751 Processing helix chain 'E' and resid 761 through 770 removed outlier: 4.231A pdb=" N PHE E 765 " --> pdb=" O PHE E 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 795 through 806 Processing helix chain 'E' and resid 814 through 826 removed outlier: 3.817A pdb=" N ASN E 818 " --> pdb=" O ASP E 814 " (cutoff:3.500A) Processing helix chain 'E' and resid 829 through 836 Processing helix chain 'E' and resid 842 through 863 removed outlier: 4.079A pdb=" N LYS E 846 " --> pdb=" O ASN E 842 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS E 853 " --> pdb=" O ASN E 849 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N CYS E 855 " --> pdb=" O SER E 851 " (cutoff:3.500A) Processing helix chain 'E' and resid 872 through 880 Processing helix chain 'E' and resid 880 through 890 Processing helix chain 'E' and resid 897 through 910 removed outlier: 3.812A pdb=" N ALA E 910 " --> pdb=" O TYR E 906 " (cutoff:3.500A) Processing helix chain 'E' and resid 926 through 940 Processing helix chain 'E' and resid 945 through 962 Processing helix chain 'E' and resid 965 through 973 Processing helix chain 'E' and resid 993 through 1004 removed outlier: 4.487A pdb=" N VAL E 997 " --> pdb=" O SER E 993 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU E1004 " --> pdb=" O LYS E1000 " (cutoff:3.500A) Processing helix chain 'E' and resid 1009 through 1026 removed outlier: 4.412A pdb=" N ASN E1025 " --> pdb=" O THR E1021 " (cutoff:3.500A) Processing helix chain 'E' and resid 1032 through 1035 removed outlier: 3.512A pdb=" N LYS E1035 " --> pdb=" O ILE E1032 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1032 through 1035' Processing helix chain 'E' and resid 1036 through 1049 removed outlier: 4.324A pdb=" N VAL E1040 " --> pdb=" O ASP E1036 " (cutoff:3.500A) Processing helix chain 'E' and resid 1050 through 1055 removed outlier: 3.568A pdb=" N PHE E1054 " --> pdb=" O LYS E1051 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN E1055 " --> pdb=" O LYS E1052 " (cutoff:3.500A) Processing helix chain 'E' and resid 1062 through 1088 removed outlier: 4.061A pdb=" N ARG E1077 " --> pdb=" O LYS E1073 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN E1088 " --> pdb=" O LEU E1084 " (cutoff:3.500A) Processing helix chain 'E' and resid 1093 through 1100 removed outlier: 4.062A pdb=" N LEU E1097 " --> pdb=" O ASN E1093 " (cutoff:3.500A) Processing helix chain 'E' and resid 1105 through 1114 removed outlier: 3.779A pdb=" N HIS E1110 " --> pdb=" O PHE E1106 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N HIS E1111 " --> pdb=" O GLU E1107 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE E1112 " --> pdb=" O LEU E1108 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE E1113 " --> pdb=" O VAL E1109 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN E1114 " --> pdb=" O HIS E1110 " (cutoff:3.500A) Processing helix chain 'E' and resid 1119 through 1132 removed outlier: 3.595A pdb=" N HIS E1123 " --> pdb=" O ASN E1119 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ASN E1127 " --> pdb=" O HIS E1123 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS E1131 " --> pdb=" O ASN E1127 " (cutoff:3.500A) Processing helix chain 'E' and resid 1138 through 1142 Processing helix chain 'E' and resid 1148 through 1152 removed outlier: 3.683A pdb=" N ASN E1151 " --> pdb=" O SER E1148 " (cutoff:3.500A) Processing helix chain 'E' and resid 1159 through 1167 Processing helix chain 'E' and resid 1170 through 1175 removed outlier: 3.774A pdb=" N ASN E1174 " --> pdb=" O ASP E1170 " (cutoff:3.500A) Processing helix chain 'E' and resid 1183 through 1215 removed outlier: 4.425A pdb=" N LEU E1194 " --> pdb=" O ALA E1190 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLN E1195 " --> pdb=" O SER E1191 " (cutoff:3.500A) Processing helix chain 'E' and resid 1223 through 1239 removed outlier: 4.477A pdb=" N VAL E1227 " --> pdb=" O ASN E1223 " (cutoff:3.500A) Processing helix chain 'E' and resid 1248 through 1267 removed outlier: 3.595A pdb=" N LEU E1252 " --> pdb=" O THR E1248 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER E1264 " --> pdb=" O TYR E1260 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU E1267 " --> pdb=" O TYR E1263 " (cutoff:3.500A) Processing helix chain 'E' and resid 1273 through 1289 removed outlier: 3.708A pdb=" N ILE E1277 " --> pdb=" O LYS E1273 " (cutoff:3.500A) Processing helix chain 'E' and resid 1304 through 1307 removed outlier: 4.137A pdb=" N PHE E1307 " --> pdb=" O LYS E1304 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1304 through 1307' Processing helix chain 'E' and resid 1308 through 1320 removed outlier: 3.871A pdb=" N GLU E1320 " --> pdb=" O LEU E1316 " (cutoff:3.500A) Processing helix chain 'E' and resid 1328 through 1358 removed outlier: 4.268A pdb=" N LYS E1346 " --> pdb=" O LEU E1342 " (cutoff:3.500A) Processing helix chain 'E' and resid 1382 through 1387 Processing helix chain 'E' and resid 1387 through 1398 Processing helix chain 'E' and resid 1401 through 1416 Processing helix chain 'E' and resid 1418 through 1431 removed outlier: 3.814A pdb=" N LEU E1430 " --> pdb=" O SER E1426 " (cutoff:3.500A) Processing helix chain 'E' and resid 1439 through 1452 removed outlier: 4.182A pdb=" N THR E1443 " --> pdb=" O LEU E1439 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU E1444 " --> pdb=" O GLY E1440 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N THR E1445 " --> pdb=" O GLN E1441 " (cutoff:3.500A) Processing helix chain 'E' and resid 1454 through 1461 Processing helix chain 'E' and resid 1465 through 1471 Processing helix chain 'E' and resid 1472 through 1480 Processing helix chain 'E' and resid 1488 through 1509 removed outlier: 3.864A pdb=" N HIS E1492 " --> pdb=" O SER E1488 " (cutoff:3.500A) Processing helix chain 'E' and resid 1514 through 1538 removed outlier: 4.413A pdb=" N LYS E1527 " --> pdb=" O SER E1523 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLN E1528 " --> pdb=" O TYR E1524 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP E1538 " --> pdb=" O TYR E1534 " (cutoff:3.500A) Processing helix chain 'E' and resid 1544 through 1558 removed outlier: 4.028A pdb=" N ILE E1548 " --> pdb=" O SER E1544 " (cutoff:3.500A) Processing helix chain 'E' and resid 1559 through 1564 removed outlier: 3.989A pdb=" N LEU E1564 " --> pdb=" O MET E1560 " (cutoff:3.500A) Processing helix chain 'E' and resid 1591 through 1607 removed outlier: 3.908A pdb=" N LYS E1595 " --> pdb=" O SER E1591 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR E1607 " --> pdb=" O SER E1603 " (cutoff:3.500A) Processing helix chain 'E' and resid 1608 through 1616 removed outlier: 3.552A pdb=" N ILE E1616 " --> pdb=" O LEU E1612 " (cutoff:3.500A) Processing helix chain 'E' and resid 1620 through 1629 Processing helix chain 'E' and resid 1632 through 1655 Processing helix chain 'F' and resid 5 through 14 Processing helix chain 'F' and resid 21 through 28 removed outlier: 3.579A pdb=" N LYS F 26 " --> pdb=" O PHE F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 34 Processing helix chain 'F' and resid 45 through 51 Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.857A pdb=" N ILE F 71 " --> pdb=" O ASN F 67 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU F 80 " --> pdb=" O SER F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 94 Processing helix chain 'F' and resid 101 through 122 removed outlier: 4.147A pdb=" N ASN F 122 " --> pdb=" O SER F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 135 Processing helix chain 'F' and resid 139 through 169 removed outlier: 3.660A pdb=" N ASN F 143 " --> pdb=" O ALA F 139 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU F 168 " --> pdb=" O LYS F 164 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU F 169 " --> pdb=" O ALA F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 200 removed outlier: 3.962A pdb=" N ILE F 179 " --> pdb=" O PHE F 175 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE F 185 " --> pdb=" O PHE F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 220 removed outlier: 3.826A pdb=" N ILE F 213 " --> pdb=" O ASN F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 removed outlier: 4.159A pdb=" N ILE F 231 " --> pdb=" O ASP F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 241 removed outlier: 4.040A pdb=" N PHE F 237 " --> pdb=" O TYR F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 259 removed outlier: 3.589A pdb=" N VAL F 252 " --> pdb=" O PRO F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 287 removed outlier: 3.544A pdb=" N LYS F 274 " --> pdb=" O THR F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 306 removed outlier: 4.444A pdb=" N PHE F 302 " --> pdb=" O ASP F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 317 Processing helix chain 'F' and resid 318 through 327 Processing helix chain 'F' and resid 424 through 443 removed outlier: 3.989A pdb=" N GLN F 428 " --> pdb=" O SER F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 459 removed outlier: 4.800A pdb=" N GLU F 457 " --> pdb=" O ILE F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 489 Processing helix chain 'F' and resid 493 through 499 Processing helix chain 'F' and resid 500 through 502 No H-bonds generated for 'chain 'F' and resid 500 through 502' Processing helix chain 'F' and resid 505 through 514 Processing helix chain 'F' and resid 519 through 534 Processing helix chain 'F' and resid 536 through 549 removed outlier: 4.159A pdb=" N GLY F 548 " --> pdb=" O TYR F 544 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU F 549 " --> pdb=" O HIS F 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 570 Processing helix chain 'F' and resid 578 through 582 removed outlier: 4.081A pdb=" N GLN F 581 " --> pdb=" O LYS F 578 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE F 582 " --> pdb=" O ARG F 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 578 through 582' Processing helix chain 'F' and resid 602 through 621 Processing helix chain 'F' and resid 625 through 633 removed outlier: 4.580A pdb=" N LEU F 631 " --> pdb=" O LYS F 628 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 643 Processing helix chain 'F' and resid 651 through 657 Processing helix chain 'F' and resid 665 through 679 removed outlier: 3.557A pdb=" N THR F 669 " --> pdb=" O GLU F 665 " (cutoff:3.500A) Processing helix chain 'F' and resid 687 through 696 Processing helix chain 'F' and resid 703 through 718 removed outlier: 3.864A pdb=" N LEU F 707 " --> pdb=" O TYR F 703 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN F 715 " --> pdb=" O GLN F 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 750 through 758 removed outlier: 4.182A pdb=" N ASP F 754 " --> pdb=" O TRP F 750 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR F 755 " --> pdb=" O PRO F 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 771 through 776 Processing helix chain 'F' and resid 785 through 790 removed outlier: 3.707A pdb=" N LEU F 788 " --> pdb=" O TYR F 785 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS F 789 " --> pdb=" O THR F 786 " (cutoff:3.500A) Processing helix chain 'F' and resid 835 through 841 Processing helix chain 'F' and resid 849 through 853 removed outlier: 3.928A pdb=" N ILE F 853 " --> pdb=" O GLN F 850 " (cutoff:3.500A) Processing helix chain 'F' and resid 860 through 872 removed outlier: 3.847A pdb=" N LEU F 864 " --> pdb=" O ASN F 860 " (cutoff:3.500A) Processing helix chain 'F' and resid 873 through 875 No H-bonds generated for 'chain 'F' and resid 873 through 875' Processing helix chain 'F' and resid 893 through 897 Processing helix chain 'F' and resid 911 through 915 Processing helix chain 'F' and resid 926 through 930 Processing helix chain 'F' and resid 936 through 950 removed outlier: 4.500A pdb=" N ASN F 940 " --> pdb=" O ILE F 936 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER F 941 " --> pdb=" O LEU F 937 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU F 945 " --> pdb=" O SER F 941 " (cutoff:3.500A) Processing helix chain 'F' and resid 965 through 969 Processing helix chain 'F' and resid 974 through 987 Processing helix chain 'F' and resid 998 through 1011 removed outlier: 3.668A pdb=" N LEU F1002 " --> pdb=" O LEU F 998 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER F1011 " --> pdb=" O THR F1007 " (cutoff:3.500A) Processing helix chain 'F' and resid 1020 through 1025 Processing helix chain 'F' and resid 1048 through 1053 Processing helix chain 'F' and resid 1069 through 1088 removed outlier: 4.005A pdb=" N MET F1073 " --> pdb=" O ASP F1069 " (cutoff:3.500A) Processing helix chain 'F' and resid 1093 through 1103 Processing helix chain 'F' and resid 1105 through 1111 Processing helix chain 'F' and resid 1137 through 1141 removed outlier: 3.504A pdb=" N SER F1141 " --> pdb=" O PHE F1138 " (cutoff:3.500A) Processing helix chain 'F' and resid 1143 through 1169 Processing helix chain 'F' and resid 1212 through 1217 removed outlier: 3.707A pdb=" N ILE F1215 " --> pdb=" O THR F1212 " (cutoff:3.500A) Processing helix chain 'F' and resid 1238 through 1255 removed outlier: 4.037A pdb=" N MET F1242 " --> pdb=" O ASP F1238 " (cutoff:3.500A) Processing helix chain 'F' and resid 1270 through 1303 removed outlier: 4.672A pdb=" N ASP F1276 " --> pdb=" O LEU F1272 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE F1290 " --> pdb=" O PHE F1286 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU F1303 " --> pdb=" O ASN F1299 " (cutoff:3.500A) Processing helix chain 'F' and resid 1309 through 1314 Processing helix chain 'F' and resid 1347 through 1364 Processing helix chain 'F' and resid 1380 through 1386 removed outlier: 3.636A pdb=" N PHE F1385 " --> pdb=" O LEU F1381 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS F1386 " --> pdb=" O TYR F1382 " (cutoff:3.500A) Processing helix chain 'F' and resid 1387 through 1389 No H-bonds generated for 'chain 'F' and resid 1387 through 1389' Processing helix chain 'F' and resid 1400 through 1415 removed outlier: 3.959A pdb=" N ARG F1415 " --> pdb=" O HIS F1411 " (cutoff:3.500A) Processing helix chain 'F' and resid 1421 through 1431 removed outlier: 3.809A pdb=" N LYS F1425 " --> pdb=" O VAL F1421 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP F1429 " --> pdb=" O LYS F1425 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG F1431 " --> pdb=" O LEU F1427 " (cutoff:3.500A) Processing helix chain 'F' and resid 1434 through 1443 Processing helix chain 'F' and resid 1452 through 1471 Processing helix chain 'F' and resid 1474 through 1480 Processing helix chain 'F' and resid 1484 through 1494 removed outlier: 3.636A pdb=" N ILE F1488 " --> pdb=" O ARG F1484 " (cutoff:3.500A) Processing helix chain 'F' and resid 1509 through 1527 Processing helix chain 'F' and resid 1533 through 1540 Processing helix chain 'F' and resid 1543 through 1550 removed outlier: 3.515A pdb=" N ILE F1547 " --> pdb=" O LEU F1543 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU F1550 " --> pdb=" O ILE F1546 " (cutoff:3.500A) Processing helix chain 'F' and resid 1551 through 1554 Processing helix chain 'F' and resid 1594 through 1611 Proline residue: F1603 - end of helix removed outlier: 3.607A pdb=" N VAL F1611 " --> pdb=" O LEU F1607 " (cutoff:3.500A) Processing helix chain 'F' and resid 1620 through 1633 removed outlier: 3.870A pdb=" N TYR F1633 " --> pdb=" O LEU F1629 " (cutoff:3.500A) Processing helix chain 'F' and resid 1634 through 1636 No H-bonds generated for 'chain 'F' and resid 1634 through 1636' Processing helix chain 'F' and resid 1637 through 1644 Processing helix chain 'F' and resid 1656 through 1675 Processing helix chain 'G' and resid 272 through 359 Proline residue: G 309 - end of helix removed outlier: 5.124A pdb=" N SER G 338 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU G 339 " --> pdb=" O SER G 335 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE G 340 " --> pdb=" O PHE G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 408 Processing helix chain 'G' and resid 437 through 470 Processing helix chain 'H' and resid 288 through 299 Processing helix chain 'H' and resid 331 through 340 Processing helix chain 'H' and resid 354 through 423 Processing helix chain 'H' and resid 430 through 448 removed outlier: 4.051A pdb=" N LYS H 435 " --> pdb=" O ILE H 431 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N MET H 436 " --> pdb=" O ALA H 432 " (cutoff:3.500A) Processing helix chain 'H' and resid 449 through 476 Processing helix chain 'H' and resid 510 through 536 Processing helix chain 'I' and resid 638 through 726 Processing helix chain 'I' and resid 741 through 776 removed outlier: 3.661A pdb=" N TYR I 745 " --> pdb=" O ARG I 741 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP I 752 " --> pdb=" O ALA I 748 " (cutoff:3.500A) Processing helix chain 'I' and resid 793 through 820 removed outlier: 4.139A pdb=" N HIS I 800 " --> pdb=" O ILE I 796 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE I 801 " --> pdb=" O LEU I 797 " (cutoff:3.500A) Processing helix chain 'J' and resid 272 through 335 Proline residue: J 309 - end of helix Processing helix chain 'J' and resid 339 through 359 Processing helix chain 'J' and resid 366 through 379 removed outlier: 3.667A pdb=" N ASP J 370 " --> pdb=" O SER J 366 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 380 through 408 removed outlier: 3.509A pdb=" N LEU J 384 " --> pdb=" O TYR J 380 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE J 390 " --> pdb=" O ASP J 386 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU J 391 " --> pdb=" O TYR J 387 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR J 396 " --> pdb=" O SER J 392 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA J 397 " --> pdb=" O ASP J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 439 through 468 removed outlier: 3.746A pdb=" N VAL J 443 " --> pdb=" O ILE J 439 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS J 465 " --> pdb=" O HIS J 461 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N THR J 466 " --> pdb=" O GLN J 462 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 298 Processing helix chain 'K' and resid 331 through 339 Processing helix chain 'K' and resid 354 through 393 Processing helix chain 'K' and resid 397 through 422 removed outlier: 3.769A pdb=" N SER K 403 " --> pdb=" O LEU K 399 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASN K 405 " --> pdb=" O ALA K 401 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL K 406 " --> pdb=" O GLN K 402 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU K 407 " --> pdb=" O SER K 403 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR K 421 " --> pdb=" O THR K 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 432 through 446 removed outlier: 4.345A pdb=" N GLN K 439 " --> pdb=" O LYS K 435 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE K 440 " --> pdb=" O MET K 436 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN K 441 " --> pdb=" O TRP K 437 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG K 446 " --> pdb=" O THR K 442 " (cutoff:3.500A) Processing helix chain 'K' and resid 458 through 465 removed outlier: 4.208A pdb=" N ARG K 462 " --> pdb=" O GLU K 458 " (cutoff:3.500A) Processing helix chain 'K' and resid 465 through 475 Processing helix chain 'K' and resid 504 through 539 Processing helix chain 'L' and resid 638 through 726 removed outlier: 3.770A pdb=" N ASP L 705 " --> pdb=" O GLU L 701 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU L 706 " --> pdb=" O ARG L 702 " (cutoff:3.500A) Processing helix chain 'L' and resid 742 through 778 removed outlier: 4.231A pdb=" N LYS L 746 " --> pdb=" O GLN L 742 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N SER L 759 " --> pdb=" O LEU L 755 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER L 760 " --> pdb=" O ASN L 756 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL L 767 " --> pdb=" O SER L 763 " (cutoff:3.500A) Processing helix chain 'L' and resid 793 through 822 Processing helix chain 'Z' and resid 13 through 31 removed outlier: 3.708A pdb=" N LEU Z 25 " --> pdb=" O LYS Z 21 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER Z 28 " --> pdb=" O GLU Z 24 " (cutoff:3.500A) Processing helix chain 'Z' and resid 44 through 60 Processing helix chain 'Z' and resid 79 through 92 removed outlier: 3.608A pdb=" N THR Z 92 " --> pdb=" O LYS Z 88 " (cutoff:3.500A) Processing helix chain 'Z' and resid 113 through 142 removed outlier: 4.156A pdb=" N ASP Z 135 " --> pdb=" O GLY Z 131 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE Z 136 " --> pdb=" O ALA Z 132 " (cutoff:3.500A) Processing helix chain 'Z' and resid 143 through 150 Processing helix chain 'Z' and resid 205 through 228 removed outlier: 3.661A pdb=" N ARG Z 209 " --> pdb=" O ASN Z 205 " (cutoff:3.500A) Processing helix chain 'Z' and resid 233 through 243 removed outlier: 4.019A pdb=" N GLU Z 237 " --> pdb=" O ASP Z 233 " (cutoff:3.500A) Processing helix chain 'Z' and resid 252 through 262 Processing helix chain 'Z' and resid 269 through 293 removed outlier: 3.566A pdb=" N VAL Z 273 " --> pdb=" O ASN Z 269 " (cutoff:3.500A) Processing helix chain 'Z' and resid 300 through 313 Processing helix chain 'Z' and resid 327 through 331 removed outlier: 3.923A pdb=" N GLY Z 330 " --> pdb=" O VAL Z 327 " (cutoff:3.500A) Processing helix chain 'Z' and resid 332 through 343 Processing helix chain 'Z' and resid 345 through 355 removed outlier: 3.846A pdb=" N ALA Z 349 " --> pdb=" O LEU Z 345 " (cutoff:3.500A) Processing helix chain 'Z' and resid 361 through 363 No H-bonds generated for 'chain 'Z' and resid 361 through 363' Processing helix chain 'Z' and resid 364 through 372 removed outlier: 3.541A pdb=" N LEU Z 368 " --> pdb=" O GLU Z 364 " (cutoff:3.500A) Processing helix chain 'Z' and resid 373 through 376 Processing helix chain 'Z' and resid 383 through 397 removed outlier: 4.219A pdb=" N LYS Z 389 " --> pdb=" O GLU Z 385 " (cutoff:3.500A) Processing helix chain 'Z' and resid 398 through 401 Processing helix chain 'Z' and resid 405 through 416 Processing helix chain 'Z' and resid 431 through 442 removed outlier: 3.523A pdb=" N TRP Z 435 " --> pdb=" O SER Z 431 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU Z 442 " --> pdb=" O MET Z 438 " (cutoff:3.500A) Processing helix chain 'Z' and resid 452 through 456 Processing helix chain 'Z' and resid 458 through 470 Processing helix chain 'Z' and resid 477 through 486 Processing helix chain 'Z' and resid 487 through 496 removed outlier: 3.557A pdb=" N ALA Z 491 " --> pdb=" O LEU Z 487 " (cutoff:3.500A) Processing helix chain 'Z' and resid 499 through 513 removed outlier: 3.702A pdb=" N LEU Z 513 " --> pdb=" O GLY Z 509 " (cutoff:3.500A) Processing helix chain 'Z' and resid 533 through 543 Processing helix chain 'Z' and resid 550 through 558 removed outlier: 3.766A pdb=" N VAL Z 558 " --> pdb=" O VAL Z 554 " (cutoff:3.500A) Processing helix chain 'Z' and resid 559 through 564 Processing helix chain 'Z' and resid 565 through 584 removed outlier: 3.956A pdb=" N LYS Z 584 " --> pdb=" O VAL Z 580 " (cutoff:3.500A) Processing helix chain 'Z' and resid 615 through 623 Processing helix chain 'Z' and resid 623 through 635 Processing helix chain 'Z' and resid 636 through 647 removed outlier: 3.695A pdb=" N SER Z 640 " --> pdb=" O ARG Z 636 " (cutoff:3.500A) Processing helix chain 'Z' and resid 649 through 667 Processing helix chain 'Z' and resid 684 through 697 removed outlier: 3.836A pdb=" N PHE Z 697 " --> pdb=" O ALA Z 693 " (cutoff:3.500A) Processing helix chain 'Z' and resid 699 through 704 removed outlier: 3.550A pdb=" N SER Z 703 " --> pdb=" O ASN Z 699 " (cutoff:3.500A) Processing helix chain 'Z' and resid 707 through 729 removed outlier: 3.821A pdb=" N LYS Z 711 " --> pdb=" O HIS Z 707 " (cutoff:3.500A) Processing helix chain 'Z' and resid 732 through 740 Processing helix chain 'Z' and resid 752 through 762 Processing helix chain 'Z' and resid 765 through 792 removed outlier: 3.525A pdb=" N LYS Z 769 " --> pdb=" O ASP Z 765 " (cutoff:3.500A) Proline residue: Z 772 - end of helix removed outlier: 5.799A pdb=" N CYS Z 781 " --> pdb=" O ILE Z 777 " (cutoff:3.500A) Processing helix chain 'Z' and resid 798 through 819 removed outlier: 3.557A pdb=" N LYS Z 807 " --> pdb=" O ILE Z 803 " (cutoff:3.500A) Processing helix chain 'Z' and resid 827 through 838 Processing sheet with id=AA1, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AA2, first strand: chain 'C' and resid 122 through 126 removed outlier: 6.847A pdb=" N ASP C 122 " --> pdb=" O GLU C 556 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N THR C 558 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN C 124 " --> pdb=" O THR C 558 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU C 560 " --> pdb=" O ASN C 124 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N SER C 126 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU C 538 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU C 535 " --> pdb=" O LYS C 513 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 138 through 145 removed outlier: 5.570A pdb=" N ARG C 140 " --> pdb=" O CYS C 613 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N CYS C 613 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN C 142 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA C 608 " --> pdb=" O THR C 605 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 161 through 166 Processing sheet with id=AA5, first strand: chain 'C' and resid 201 through 207 removed outlier: 4.016A pdb=" N ASP C 229 " --> pdb=" O THR C 226 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE C 230 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU C 251 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE C 232 " --> pdb=" O THR C 249 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 260 through 265 removed outlier: 3.634A pdb=" N ASN C 262 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE C 272 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 342 through 348 removed outlier: 6.697A pdb=" N VAL C 363 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU C 378 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N SER C 365 " --> pdb=" O PRO C 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 406 through 411 removed outlier: 6.763A pdb=" N ARG C 431 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL C 451 " --> pdb=" O ARG C 431 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N TYR C 433 " --> pdb=" O ASP C 449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 438 through 439 removed outlier: 3.549A pdb=" N SER C 442 " --> pdb=" O SER C 439 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 678 through 679 Processing sheet with id=AB2, first strand: chain 'C' and resid 729 through 732 Processing sheet with id=AB3, first strand: chain 'D' and resid 133 through 139 removed outlier: 6.026A pdb=" N GLU D 138 " --> pdb=" O PHE D 598 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE D 530 " --> pdb=" O ILE D 526 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 148 through 155 removed outlier: 6.804A pdb=" N ILE D 649 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL D 153 " --> pdb=" O ILE D 647 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE D 647 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER D 646 " --> pdb=" O THR D 643 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ARG D 638 " --> pdb=" O PRO D 610 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA D 640 " --> pdb=" O ILE D 608 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE D 608 " --> pdb=" O ALA D 640 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU D 642 " --> pdb=" O GLN D 606 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 172 through 176 removed outlier: 3.532A pdb=" N ARG D 181 " --> pdb=" O PHE D 176 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU D 190 " --> pdb=" O VAL D 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 211 through 217 removed outlier: 3.577A pdb=" N HIS D 230 " --> pdb=" O ILE D 245 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU D 239 " --> pdb=" O THR D 236 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 211 through 217 removed outlier: 3.577A pdb=" N HIS D 230 " --> pdb=" O ILE D 245 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU D 239 " --> pdb=" O THR D 236 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 270 through 276 removed outlier: 3.982A pdb=" N ASP D 272 " --> pdb=" O ALA D 285 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 281 " --> pdb=" O HIS D 276 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE D 282 " --> pdb=" O LEU D 296 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 342 through 343 Processing sheet with id=AC1, first strand: chain 'D' and resid 356 through 362 Processing sheet with id=AC2, first strand: chain 'D' and resid 420 through 425 removed outlier: 6.630A pdb=" N LEU D 439 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE D 423 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL D 437 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER D 425 " --> pdb=" O PHE D 435 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE D 435 " --> pdb=" O SER D 425 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N PHE D 448 " --> pdb=" O PHE D 435 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL D 437 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU D 446 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ARG D 445 " --> pdb=" O ILE D 465 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE D 465 " --> pdb=" O ARG D 445 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR D 447 " --> pdb=" O GLU D 463 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 452 through 453 Processing sheet with id=AC4, first strand: chain 'E' and resid 275 through 276 removed outlier: 3.759A pdb=" N ASN E 276 " --> pdb=" O GLN E 281 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 463 through 466 removed outlier: 3.743A pdb=" N ASP E 476 " --> pdb=" O GLU E 500 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 505 through 507 Processing sheet with id=AC7, first strand: chain 'F' and resid 55 through 57 removed outlier: 4.023A pdb=" N ILE F 56 " --> pdb=" O PHE F 64 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 310 through 312 3870 hydrogen bonds defined for protein. 11328 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 28.57 Time building geometry restraints manager: 15.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 11461 1.28 - 1.41: 16028 1.41 - 1.55: 40112 1.55 - 1.69: 213 1.69 - 1.82: 261 Bond restraints: 68075 Sorted by residual: bond pdb=" C LEU H 427 " pdb=" N PRO H 428 " ideal model delta sigma weight residual 1.334 1.528 -0.194 8.40e-03 1.42e+04 5.35e+02 bond pdb=" C ASN F1235 " pdb=" N ILE F1236 " ideal model delta sigma weight residual 1.332 1.533 -0.201 1.36e-02 5.41e+03 2.18e+02 bond pdb=" C LYS K 326 " pdb=" N PRO K 327 " ideal model delta sigma weight residual 1.330 1.501 -0.171 1.25e-02 6.40e+03 1.88e+02 bond pdb=" C ARG H 425 " pdb=" N GLY H 426 " ideal model delta sigma weight residual 1.331 1.487 -0.157 1.46e-02 4.69e+03 1.15e+02 bond pdb=" C ILE F1312 " pdb=" O ILE F1312 " ideal model delta sigma weight residual 1.241 1.140 0.101 1.06e-02 8.90e+03 9.17e+01 ... (remaining 68070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.68: 92141 10.68 - 21.37: 153 21.37 - 32.05: 5 32.05 - 42.73: 0 42.73 - 53.42: 1 Bond angle restraints: 92300 Sorted by residual: angle pdb=" CA PRO F1090 " pdb=" N PRO F1090 " pdb=" CD PRO F1090 " ideal model delta sigma weight residual 112.00 58.58 53.42 1.40e+00 5.10e-01 1.46e+03 angle pdb=" C ILE F 356 " pdb=" N PRO F 357 " pdb=" CA PRO F 357 " ideal model delta sigma weight residual 119.84 144.83 -24.99 1.25e+00 6.40e-01 4.00e+02 angle pdb=" C LYS K 326 " pdb=" N PRO K 327 " pdb=" CA PRO K 327 " ideal model delta sigma weight residual 120.21 136.80 -16.59 9.60e-01 1.09e+00 2.99e+02 angle pdb=" C SER F1394 " pdb=" N PRO F1395 " pdb=" CA PRO F1395 " ideal model delta sigma weight residual 119.84 138.89 -19.05 1.25e+00 6.40e-01 2.32e+02 angle pdb=" C ARG H 425 " pdb=" N GLY H 426 " pdb=" CA GLY H 426 " ideal model delta sigma weight residual 121.41 94.18 27.23 1.96e+00 2.60e-01 1.93e+02 ... (remaining 92295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 36564 17.98 - 35.97: 3701 35.97 - 53.95: 833 53.95 - 71.94: 178 71.94 - 89.92: 61 Dihedral angle restraints: 41337 sinusoidal: 15773 harmonic: 25564 Sorted by residual: dihedral pdb=" C ASN I 736 " pdb=" N ASN I 736 " pdb=" CA ASN I 736 " pdb=" CB ASN I 736 " ideal model delta harmonic sigma weight residual -122.60 -156.11 33.51 0 2.50e+00 1.60e-01 1.80e+02 dihedral pdb=" C HIS I 800 " pdb=" N HIS I 800 " pdb=" CA HIS I 800 " pdb=" CB HIS I 800 " ideal model delta harmonic sigma weight residual -122.60 -154.02 31.42 0 2.50e+00 1.60e-01 1.58e+02 dihedral pdb=" N ASN I 736 " pdb=" C ASN I 736 " pdb=" CA ASN I 736 " pdb=" CB ASN I 736 " ideal model delta harmonic sigma weight residual 122.80 153.04 -30.24 0 2.50e+00 1.60e-01 1.46e+02 ... (remaining 41334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.250: 10608 0.250 - 0.499: 234 0.499 - 0.749: 22 0.749 - 0.999: 14 0.999 - 1.248: 6 Chirality restraints: 10884 Sorted by residual: chirality pdb=" CA ASN I 736 " pdb=" N ASN I 736 " pdb=" C ASN I 736 " pdb=" CB ASN I 736 " both_signs ideal model delta sigma weight residual False 2.51 1.26 1.25 2.00e-01 2.50e+01 3.90e+01 chirality pdb=" CA HIS I 800 " pdb=" N HIS I 800 " pdb=" C HIS I 800 " pdb=" CB HIS I 800 " both_signs ideal model delta sigma weight residual False 2.51 1.30 1.21 2.00e-01 2.50e+01 3.66e+01 chirality pdb=" CA GLN F 711 " pdb=" N GLN F 711 " pdb=" C GLN F 711 " pdb=" CB GLN F 711 " both_signs ideal model delta sigma weight residual False 2.51 1.37 1.14 2.00e-01 2.50e+01 3.26e+01 ... (remaining 10881 not shown) Planarity restraints: 11817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE H 509 " -0.056 2.00e-02 2.50e+03 1.17e-01 1.36e+02 pdb=" C ILE H 509 " 0.202 2.00e-02 2.50e+03 pdb=" O ILE H 509 " -0.077 2.00e-02 2.50e+03 pdb=" N VAL H 510 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 360 " -0.050 2.00e-02 2.50e+03 1.06e-01 1.12e+02 pdb=" C LEU F 360 " 0.183 2.00e-02 2.50e+03 pdb=" O LEU F 360 " -0.072 2.00e-02 2.50e+03 pdb=" N LEU F 361 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D1162 " 0.109 2.00e-02 2.50e+03 6.71e-02 9.01e+01 pdb=" CG TYR D1162 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR D1162 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR D1162 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR D1162 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR D1162 " -0.062 2.00e-02 2.50e+03 pdb=" CZ TYR D1162 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR D1162 " 0.117 2.00e-02 2.50e+03 ... (remaining 11814 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 38 1.81 - 2.58: 1119 2.58 - 3.36: 90721 3.36 - 4.13: 162222 4.13 - 4.90: 281273 Nonbonded interactions: 535373 Sorted by model distance: nonbonded pdb=" O LEU K 481 " pdb=" O ASP K 492 " model vdw 1.041 3.040 nonbonded pdb=" CB MET K 482 " pdb=" O ASP L 783 " model vdw 1.065 3.440 nonbonded pdb=" CB ILE Z 782 " pdb=" O SER Z 838 " model vdw 1.110 3.470 nonbonded pdb=" CB LEU A 49 " pdb=" CB GLN L 792 " model vdw 1.136 3.840 nonbonded pdb=" CD GLN F 334 " pdb=" OD1 ASN F 860 " model vdw 1.172 3.270 ... (remaining 535368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 53 or (resid 54 through 56 and (name N or name \ CA or name C or name O or name CB )) or resid 57 or (resid 58 through 60 and (na \ me N or name CA or name C or name O or name CB )) or resid 79 through 136 or (re \ sid 137 and (name N or name CA or name C or name O or name CB )) or resid 138 th \ rough 210 or (resid 211 and (name N or name CA or name C or name O or name CB )) \ or resid 212 through 245 or (resid 246 and (name N or name CA or name C or name \ O or name CB )) or resid 247 through 248 or (resid 249 through 253 and (name N \ or name CA or name C or name O or name CB )) or resid 254 through 451 or (resid \ 452 and (name N or name CA or name C or name O or name CB )) or resid 453 or (re \ sid 454 and (name N or name CA or name C or name O or name CB )) or resid 455 th \ rough 616 or (resid 617 through 618 and (name N or name CA or name C or name O o \ r name CB )) or resid 619 through 628 or (resid 629 and (name N or name CA or na \ me C or name O or name CB )) or resid 630 through 650 or (resid 651 and (name N \ or name CA or name C or name O or name CB )) or resid 652 through 665 or (resid \ 666 through 667 and (name N or name CA or name C or name O or name CB )) or resi \ d 668 through 722 or (resid 723 and (name N or name CA or name C or name O or na \ me CB )) or resid 724 through 738 or (resid 739 and (name N or name CA or name C \ or name O or name CB )) or resid 740 through 745 or (resid 746 through 747 and \ (name N or name CA or name C or name O or name CB )) or resid 748 or (resid 749 \ through 751 and (name N or name CA or name C or name O or name CB )) or resid 75 \ 2 through 755 or (resid 756 through 757 and (name N or name CA or name C or name \ O or name CB )) or resid 758 or (resid 759 through 763 and (name N or name CA o \ r name C or name O or name CB )) or resid 764 through 768 or (resid 769 and (nam \ e N or name CA or name C or name O or name CB )) or resid 770 through 805 or (re \ sid 806 through 807 and (name N or name CA or name C or name O or name CB )) or \ resid 808 or (resid 809 through 812 and (name N or name CA or name C or name O o \ r name CB )) or resid 813 or (resid 814 through 817 and (name N or name CA or na \ me C or name O or name CB )) or resid 818 or (resid 819 through 821 and (name N \ or name CA or name C or name O or name CB )) or resid 822 or (resid 823 through \ 824 and (name N or name CA or name C or name O or name CB )) or resid 825 throug \ h 828 or (resid 829 and (name N or name CA or name C or name O or name CB )) or \ resid 830 through 831 or (resid 832 and (name N or name CA or name C or name O o \ r name CB )) or resid 833 through 835 or (resid 836 and (name N or name CA or na \ me C or name O or name CB )) or resid 837 or (resid 838 through 839 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'Z' and (resid 13 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 41 or (resid 42 through 44 and (na \ me N or name CA or name C or name O or name CB )) or resid 45 or (resid 46 throu \ gh 52 and (name N or name CA or name C or name O or name CB )) or resid 53 throu \ gh 55 or (resid 56 and (name N or name CA or name C or name O or name CB )) or r \ esid 57 through 59 or (resid 60 and (name N or name CA or name C or name O or na \ me CB )) or resid 79 or (resid 80 through 81 and (name N or name CA or name C or \ name O or name CB )) or resid 82 through 83 or (resid 84 through 85 and (name N \ or name CA or name C or name O or name CB )) or resid 86 or (resid 87 through 9 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 112 through \ 116 or (resid 117 through 118 and (name N or name CA or name C or name O or name \ CB )) or resid 119 through 120 or (resid 121 and (name N or name CA or name C o \ r name O or name CB )) or resid 122 or (resid 123 and (name N or name CA or name \ C or name O or name CB )) or resid 124 or (resid 125 through 127 and (name N or \ name CA or name C or name O or name CB )) or resid 128 or (resid 129 and (name \ N or name CA or name C or name O or name CB )) or resid 130 through 132 or (resi \ d 133 and (name N or name CA or name C or name O or name CB )) or resid 134 thro \ ugh 135 or (resid 136 through 137 and (name N or name CA or name C or name O or \ name CB )) or resid 138 through 141 or resid 192 through 241 or (resid 242 and ( \ name N or name CA or name C or name O or name CB )) or resid 243 through 249 or \ (resid 250 through 253 and (name N or name CA or name C or name O or name CB )) \ or resid 254 through 258 or (resid 259 and (name N or name CA or name C or name \ O or name CB )) or resid 260 through 261 or (resid 262 and (name N or name CA or \ name C or name O or name CB )) or resid 263 through 631 or (resid 632 and (name \ N or name CA or name C or name O or name CB )) or resid 633 through 760 or (res \ id 761 through 763 and (name N or name CA or name C or name O or name CB )) or r \ esid 764 through 779 or (resid 780 and (name N or name CA or name C or name O or \ name CB )) or resid 781 through 785 or (resid 786 and (name N or name CA or nam \ e C or name O or name CB )) or resid 787 through 823 or (resid 824 and (name N o \ r name CA or name C or name O or name CB )) or resid 825 through 839)) } ncs_group { reference = (chain 'G' and (resid 271 through 293 or (resid 294 and (name N or name CA or na \ me C or name O or name CB )) or resid 295 through 297 or (resid 298 and (name N \ or name CA or name C or name O or name CB )) or resid 299 through 332 or (resid \ 333 and (name N or name CA or name C or name O or name CB )) or resid 334 throug \ h 335 or (resid 336 and (name N or name CA or name C or name O or name CB )) or \ resid 337 through 338 or (resid 339 and (name N or name CA or name C or name O o \ r name CB )) or resid 340 through 386 or (resid 387 and (name N or name CA or na \ me C or name O or name CB )) or resid 388 through 422 or (resid 428 through 433 \ and (name N or name CA or name C or name O or name CB )) or resid 434 through 43 \ 9 or (resid 440 and (name N or name CA or name C or name O or name CB )) or resi \ d 441 or (resid 442 and (name N or name CA or name C or name O or name CB )) or \ resid 443 through 446 or (resid 447 and (name N or name CA or name C or name O o \ r name CB )) or resid 448 through 450 or (resid 451 through 454 and (name N or n \ ame CA or name C or name O or name CB )) or resid 455 through 470)) selection = (chain 'J' and (resid 271 through 356 or (resid 357 and (name N or name CA or na \ me C or name O or name CB )) or resid 358 through 395 or (resid 396 through 397 \ and (name N or name CA or name C or name O or name CB )) or resid 398 through 42 \ 9 or (resid 430 through 433 and (name N or name CA or name C or name O or name C \ B )) or resid 434 through 444 or (resid 445 and (name N or name CA or name C or \ name O or name CB )) or resid 446 through 451 or (resid 452 through 454 and (nam \ e N or name CA or name C or name O or name CB )) or resid 455 or (resid 456 and \ (name N or name CA or name C or name O or name CB )) or resid 457 through 460 or \ (resid 461 through 464 and (name N or name CA or name C or name O or name CB )) \ or resid 465 through 470)) } ncs_group { reference = (chain 'H' and ((resid 287 and (name N or name CA or name C or name O or name CB \ )) or resid 288 through 290 or (resid 291 and (name N or name CA or name C or n \ ame O or name CB )) or resid 292 through 297 or (resid 298 and (name N or name C \ A or name C or name O or name CB )) or resid 299 through 302 or (resid 303 and ( \ name N or name CA or name C or name O or name CB )) or resid 304 through 315 or \ (resid 316 through 323 and (name N or name CA or name C or name O or name CB )) \ or resid 324 through 380 or (resid 381 through 383 and (name N or name CA or nam \ e C or name O or name CB )) or resid 384 through 385 or (resid 386 and (name N o \ r name CA or name C or name O or name CB )) or resid 387 through 388 or (resid 3 \ 89 through 392 and (name N or name CA or name C or name O or name CB )) or resid \ 393 through 430 or (resid 431 through 432 and (name N or name CA or name C or n \ ame O or name CB )) or resid 433 through 434 or (resid 435 and (name N or name C \ A or name C or name O or name CB )) or resid 436 through 440 or (resid 441 and ( \ name N or name CA or name C or name O or name CB )) or resid 442 through 443 or \ (resid 444 through 445 and (name N or name CA or name C or name O or name CB )) \ or resid 446 or (resid 447 and (name N or name CA or name C or name O or name CB \ )) or resid 448 through 449 or (resid 450 through 451 and (name N or name CA or \ name C or name O or name CB )) or resid 452 through 455 or (resid 456 and (name \ N or name CA or name C or name O or name CB )) or resid 457 or (resid 458 throu \ gh 465 and (name N or name CA or name C or name O or name CB )) or resid 466 thr \ ough 467 or (resid 468 and (name N or name CA or name C or name O or name CB )) \ or resid 469 through 474 or (resid 475 through 506 and (name N or name CA or nam \ e C or name O or name CB )) or resid 507 through 523 or (resid 524 through 528 a \ nd (name N or name CA or name C or name O or name CB )) or resid 529 through 533 \ or (resid 534 through 535 and (name N or name CA or name C or name O or name CB \ )) or resid 536 through 537 or (resid 538 through 540 and (name N or name CA or \ name C or name O or name CB )))) selection = (chain 'K' and (resid 287 through 314 or (resid 315 through 323 and (name N or n \ ame CA or name C or name O or name CB )) or resid 324 through 330 or (resid 331 \ and (name N or name CA or name C or name O or name CB )) or resid 332 through 39 \ 0 or (resid 391 through 392 and (name N or name CA or name C or name O or name C \ B )) or resid 393 through 403 or (resid 404 and (name N or name CA or name C or \ name O or name CB )) or resid 405 through 406 or (resid 407 and (name N or name \ CA or name C or name O or name CB )) or resid 408 through 416 or (resid 417 and \ (name N or name CA or name C or name O or name CB )) or resid 418 or (resid 419 \ through 425 and (name N or name CA or name C or name O or name CB )) or resid 42 \ 6 or (resid 427 and (name N or name CA or name C or name O or name CB )) or resi \ d 428 through 466 or (resid 467 through 468 and (name N or name CA or name C or \ name O or name CB )) or resid 469 through 493 or (resid 502 through 506 and (nam \ e N or name CA or name C or name O or name CB )) or resid 507 through 508 or (re \ sid 509 and (name N or name CA or name C or name O or name CB )) or resid 510 or \ (resid 511 and (name N or name CA or name C or name O or name CB )) or resid 51 \ 2 or (resid 513 through 518 and (name N or name CA or name C or name O or name C \ B )) or resid 519 or (resid 520 through 522 and (name N or name CA or name C or \ name O or name CB )) or resid 523 through 524 or (resid 525 through 528 and (nam \ e N or name CA or name C or name O or name CB )) or resid 529 through 538 or (re \ sid 539 through 540 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'I' and (resid 637 through 654 or (resid 655 and (name N or name CA or na \ me C or name O or name CB )) or resid 656 through 658 or (resid 659 and (name N \ or name CA or name C or name O or name CB )) or resid 660 through 689 or (resid \ 690 and (name N or name CA or name C or name O or name CB )) or resid 691 throug \ h 696 or (resid 697 through 698 and (name N or name CA or name C or name O or na \ me CB )) or resid 699 through 700 or (resid 701 and (name N or name CA or name C \ or name O or name CB )) or resid 702 through 735 or (resid 736 and (name N or n \ ame CA or name C or name O or name CB )) or resid 737 through 739 or (resid 740 \ through 742 and (name N or name CA or name C or name O or name CB )) or resid 74 \ 3 through 763 or (resid 764 through 765 and (name N or name CA or name C or name \ O or name CB )) or resid 766 through 767 or (resid 768 and (name N or name CA o \ r name C or name O or name CB )) or resid 769 through 774 or (resid 775 through \ 794 and (name N or name CA or name C or name O or name CB )) or resid 795 throug \ h 814 or (resid 815 and (name N or name CA or name C or name O or name CB )) or \ resid 816 through 817 or (resid 818 and (name N or name CA or name C or name O o \ r name CB )) or resid 819 through 821 or (resid 822 and (name N or name CA or na \ me C or name O or name CB )) or resid 823)) selection = (chain 'L' and (resid 637 through 723 or (resid 724 through 725 and (name N or n \ ame CA or name C or name O or name CB )) or resid 726 through 734 or (resid 735 \ through 736 and (name N or name CA or name C or name O or name CB )) or resid 73 \ 7 through 738 or (resid 739 through 742 and (name N or name CA or name C or name \ O or name CB )) or resid 743 through 772 or (resid 773 and (name N or name CA o \ r name C or name O or name CB )) or resid 774 through 776 or (resid 777 through \ 794 and (name N or name CA or name C or name O or name CB )) or resid 795 throug \ h 803 or (resid 804 through 805 and (name N or name CA or name C or name O or na \ me CB )) or resid 806 through 810 or (resid 811 and (name N or name CA or name C \ or name O or name CB )) or resid 812 through 819 or (resid 820 and (name N or n \ ame CA or name C or name O or name CB )) or resid 821 through 823)) } 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: 2.700 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: 0.060 Extract box with map and model: 2.030 Check model and map are aligned: 0.370 Set scattering table: 0.480 Process input model: 119.070 Find NCS groups from input model: 2.880 Set up NCS constraints: 0.340 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: 0.020 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4448 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 : 0.010 0.201 68075 Z= 0.675 Angle : 1.686 53.418 92300 Z= 1.061 Chirality : 0.100 1.248 10884 Planarity : 0.011 0.145 11817 Dihedral : 15.855 89.924 24661 Min Nonbonded Distance : 1.041 Molprobity Statistics. All-atom Clashscore : 23.12 Ramachandran Plot: Outliers : 2.21 % Allowed : 9.32 % Favored : 88.47 % Rotamer: Outliers : 4.33 % Allowed : 8.11 % Favored : 87.56 % Cbeta Deviations : 1.67 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.08), residues: 8584 helix: -1.43 (0.07), residues: 4971 sheet: -0.30 (0.26), residues: 348 loop : -3.20 (0.10), residues: 3265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.006 TRP F 672 HIS 0.018 0.003 HIS C 536 PHE 0.095 0.006 PHE J 372 TYR 0.117 0.007 TYR D1162 ARG 0.023 0.002 ARG F 668 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1382 residues out of total 7900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 1069 time to evaluate : 5.713 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: A 119 GLU cc_start: 0.5079 (OUTLIER) cc_final: 0.3147 (tt0) REVERT: A 197 GLU cc_start: 0.4288 (mt-10) cc_final: 0.3944 (tt0) REVERT: A 438 MET cc_start: 0.0352 (pmm) cc_final: -0.0447 (mtt) REVERT: C 318 ILE cc_start: 0.0570 (OUTLIER) cc_final: 0.0264 (tp) REVERT: C 388 MET cc_start: -0.0515 (mmm) cc_final: -0.2009 (ptm) REVERT: C 495 THR cc_start: 0.2357 (m) cc_final: 0.1698 (p) REVERT: C 695 ASP cc_start: -0.1250 (OUTLIER) cc_final: -0.1527 (t0) REVERT: C 861 GLN cc_start: 0.4938 (tt0) cc_final: 0.4732 (mm-40) REVERT: C 910 LEU cc_start: -0.4648 (OUTLIER) cc_final: -0.4913 (mt) REVERT: C 1104 LYS cc_start: 0.1097 (tttt) cc_final: 0.0380 (mmmt) REVERT: C 1278 ASP cc_start: 0.2831 (p0) cc_final: 0.1798 (m-30) REVERT: C 1310 MET cc_start: -0.0321 (mtt) cc_final: -0.0878 (mtm) REVERT: D 199 ASN cc_start: 0.3720 (m-40) cc_final: 0.3031 (t0) REVERT: D 327 MET cc_start: 0.1153 (mmm) cc_final: 0.0807 (ttt) REVERT: D 493 PHE cc_start: 0.5060 (p90) cc_final: 0.4740 (p90) REVERT: D 669 PHE cc_start: 0.2415 (t80) cc_final: 0.2163 (t80) REVERT: D 1000 ASP cc_start: -0.0003 (OUTLIER) cc_final: -0.0627 (t70) REVERT: E 121 ASP cc_start: 0.6435 (m-30) cc_final: 0.5838 (p0) REVERT: E 187 PHE cc_start: 0.6473 (t80) cc_final: 0.6137 (t80) REVERT: E 284 ILE cc_start: 0.7263 (mm) cc_final: 0.6933 (mm) REVERT: E 445 LEU cc_start: 0.8567 (mt) cc_final: 0.8365 (mt) REVERT: E 648 ARG cc_start: 0.6886 (mtt90) cc_final: 0.6183 (ptt-90) REVERT: E 771 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.4905 (mt) REVERT: E 808 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8922 (p) REVERT: E 842 ASN cc_start: 0.6982 (m-40) cc_final: 0.6666 (t0) REVERT: E 980 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6255 (pptt) REVERT: E 1028 THR cc_start: 0.5791 (p) cc_final: 0.5439 (p) REVERT: E 1123 HIS cc_start: 0.7239 (m-70) cc_final: 0.6869 (t-90) REVERT: E 1182 ASN cc_start: 0.3201 (p0) cc_final: 0.2449 (p0) REVERT: F 334 GLN cc_start: 0.3580 (OUTLIER) cc_final: -0.0180 (pp30) REVERT: F 522 MET cc_start: -0.0304 (ppp) cc_final: -0.0533 (tmm) REVERT: F 715 ASN cc_start: 0.5482 (t0) cc_final: 0.5144 (t0) REVERT: F 782 LYS cc_start: 0.1097 (OUTLIER) cc_final: 0.0691 (mmtt) REVERT: F 888 PRO cc_start: 0.3959 (OUTLIER) cc_final: 0.3520 (Cg_exo) REVERT: F 970 ASP cc_start: 0.5096 (t0) cc_final: 0.4880 (p0) REVERT: F 1027 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7589 (tm-30) REVERT: F 1083 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8180 (mt) REVERT: F 1118 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7645 (tpp80) REVERT: F 1128 ASP cc_start: 0.3610 (OUTLIER) cc_final: 0.3341 (m-30) REVERT: F 1156 TYR cc_start: 0.6353 (t80) cc_final: 0.4397 (m-80) REVERT: F 1159 GLN cc_start: 0.6469 (OUTLIER) cc_final: 0.5810 (mt0) REVERT: F 1169 SER cc_start: 0.6568 (OUTLIER) cc_final: 0.6281 (m) REVERT: F 1293 ASN cc_start: 0.6069 (OUTLIER) cc_final: 0.5516 (t0) REVERT: F 1314 VAL cc_start: 0.7041 (OUTLIER) cc_final: 0.6448 (p) REVERT: F 1356 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7076 (tp) REVERT: F 1372 THR cc_start: 0.5628 (OUTLIER) cc_final: 0.3648 (t) REVERT: F 1373 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.5843 (t0) REVERT: F 1382 TYR cc_start: 0.5271 (t80) cc_final: 0.3141 (m-80) REVERT: F 1387 THR cc_start: 0.7180 (OUTLIER) cc_final: 0.6950 (t) REVERT: G 405 LEU cc_start: 0.8020 (tt) cc_final: 0.7196 (mt) REVERT: H 358 LEU cc_start: 0.3211 (mt) cc_final: 0.2926 (tp) REVERT: H 398 ILE cc_start: 0.5508 (OUTLIER) cc_final: 0.5218 (mt) REVERT: H 442 THR cc_start: 0.8160 (m) cc_final: 0.7822 (t) REVERT: I 662 ILE cc_start: 0.7092 (tt) cc_final: 0.6866 (tt) REVERT: I 764 SER cc_start: 0.7502 (m) cc_final: 0.6975 (p) REVERT: I 778 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6748 (tttp) REVERT: I 808 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8446 (p0) REVERT: J 444 ILE cc_start: 0.5438 (OUTLIER) cc_final: 0.5050 (tp) REVERT: K 423 LYS cc_start: 0.2230 (OUTLIER) cc_final: 0.1801 (tppt) REVERT: K 446 ARG cc_start: 0.5405 (OUTLIER) cc_final: 0.5121 (ttp80) REVERT: L 703 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.6188 (pp30) REVERT: Z 20 LYS cc_start: 0.4252 (OUTLIER) cc_final: 0.3251 (mmtt) REVERT: Z 122 LEU cc_start: 0.4138 (OUTLIER) cc_final: 0.2540 (mp) REVERT: Z 129 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6978 (tp) REVERT: Z 139 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7069 (t80) REVERT: Z 302 VAL cc_start: 0.3383 (t) cc_final: 0.3146 (t) REVERT: Z 459 LEU cc_start: 0.6745 (tp) cc_final: 0.6110 (tt) REVERT: Z 541 TYR cc_start: 0.7370 (t80) cc_final: 0.6959 (t80) REVERT: Z 661 LEU cc_start: 0.8409 (mt) cc_final: 0.8093 (mp) REVERT: Z 715 MET cc_start: 0.5384 (mmp) cc_final: 0.5056 (ppp) REVERT: Z 716 LEU cc_start: 0.8189 (tt) cc_final: 0.7877 (tp) REVERT: Z 765 ASP cc_start: 0.1939 (OUTLIER) cc_final: 0.1445 (m-30) outliers start: 313 outliers final: 130 residues processed: 1360 average time/residue: 0.6911 time to fit residues: 1622.8036 Evaluate side-chains 733 residues out of total 7900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 568 time to evaluate : 5.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 130 ASN Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 577 PHE Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain C residue 896 CYS Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 1299 LYS Chi-restraints excluded: chain C residue 1301 SER Chi-restraints excluded: chain C residue 1387 HIS Chi-restraints excluded: chain D residue 528 PRO Chi-restraints excluded: chain D residue 980 SER Chi-restraints excluded: chain D residue 984 THR Chi-restraints excluded: chain D residue 990 GLU Chi-restraints excluded: chain D residue 1000 ASP Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 771 LEU Chi-restraints excluded: chain E residue 773 LEU Chi-restraints excluded: chain E residue 808 THR Chi-restraints excluded: chain E residue 895 HIS Chi-restraints excluded: chain E residue 923 LEU Chi-restraints excluded: chain E residue 980 LYS Chi-restraints excluded: chain E residue 1026 THR Chi-restraints excluded: chain E residue 1079 VAL Chi-restraints excluded: chain E residue 1514 VAL Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 334 GLN Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 397 MET Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain F residue 782 LYS Chi-restraints excluded: chain F residue 836 ILE Chi-restraints excluded: chain F residue 837 TYR Chi-restraints excluded: chain F residue 888 PRO Chi-restraints excluded: chain F residue 900 LEU Chi-restraints excluded: chain F residue 921 PRO Chi-restraints excluded: chain F residue 922 LEU Chi-restraints excluded: chain F residue 926 LEU Chi-restraints excluded: chain F residue 928 LEU Chi-restraints excluded: chain F residue 950 GLU Chi-restraints excluded: chain F residue 951 ARG Chi-restraints excluded: chain F residue 958 SER Chi-restraints excluded: chain F residue 965 LEU Chi-restraints excluded: chain F residue 1027 GLN Chi-restraints excluded: chain F residue 1029 SER Chi-restraints excluded: chain F residue 1032 ILE Chi-restraints excluded: chain F residue 1060 LEU Chi-restraints excluded: chain F residue 1068 ILE Chi-restraints excluded: chain F residue 1083 ILE Chi-restraints excluded: chain F residue 1090 PRO Chi-restraints excluded: chain F residue 1092 THR Chi-restraints excluded: chain F residue 1118 ARG Chi-restraints excluded: chain F residue 1128 ASP Chi-restraints excluded: chain F residue 1144 VAL Chi-restraints excluded: chain F residue 1147 PHE Chi-restraints excluded: chain F residue 1149 SER Chi-restraints excluded: chain F residue 1150 PHE Chi-restraints excluded: chain F residue 1153 TYR Chi-restraints excluded: chain F residue 1155 ASN Chi-restraints excluded: chain F residue 1159 GLN Chi-restraints excluded: chain F residue 1165 ILE Chi-restraints excluded: chain F residue 1166 HIS Chi-restraints excluded: chain F residue 1169 SER Chi-restraints excluded: chain F residue 1181 VAL Chi-restraints excluded: chain F residue 1191 SER Chi-restraints excluded: chain F residue 1276 ASP Chi-restraints excluded: chain F residue 1277 VAL Chi-restraints excluded: chain F residue 1278 GLU Chi-restraints excluded: chain F residue 1280 ILE Chi-restraints excluded: chain F residue 1285 HIS Chi-restraints excluded: chain F residue 1291 SER Chi-restraints excluded: chain F residue 1293 ASN Chi-restraints excluded: chain F residue 1297 GLU Chi-restraints excluded: chain F residue 1300 LEU Chi-restraints excluded: chain F residue 1301 SER Chi-restraints excluded: chain F residue 1302 VAL Chi-restraints excluded: chain F residue 1309 LEU Chi-restraints excluded: chain F residue 1313 ILE Chi-restraints excluded: chain F residue 1314 VAL Chi-restraints excluded: chain F residue 1356 LEU Chi-restraints excluded: chain F residue 1358 VAL Chi-restraints excluded: chain F residue 1363 ILE Chi-restraints excluded: chain F residue 1364 TYR Chi-restraints excluded: chain F residue 1365 ASN Chi-restraints excluded: chain F residue 1372 THR Chi-restraints excluded: chain F residue 1373 ASP Chi-restraints excluded: chain F residue 1387 THR Chi-restraints excluded: chain F residue 1417 LEU Chi-restraints excluded: chain F residue 1635 ARG Chi-restraints excluded: chain F residue 1680 GLN Chi-restraints excluded: chain G residue 333 ILE Chi-restraints excluded: chain H residue 398 ILE Chi-restraints excluded: chain H residue 534 VAL Chi-restraints excluded: chain I residue 778 LYS Chi-restraints excluded: chain I residue 792 GLN Chi-restraints excluded: chain I residue 795 LYS Chi-restraints excluded: chain I residue 797 LEU Chi-restraints excluded: chain I residue 808 ASP Chi-restraints excluded: chain I residue 810 ASN Chi-restraints excluded: chain I residue 815 GLU Chi-restraints excluded: chain I residue 821 ILE Chi-restraints excluded: chain I residue 823 LYS Chi-restraints excluded: chain J residue 368 ASP Chi-restraints excluded: chain J residue 370 ASP Chi-restraints excluded: chain J residue 371 LYS Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 389 ARG Chi-restraints excluded: chain J residue 390 ILE Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 398 VAL Chi-restraints excluded: chain J residue 399 ASN Chi-restraints excluded: chain J residue 401 ILE Chi-restraints excluded: chain J residue 444 ILE Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 394 THR Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain K residue 404 ARG Chi-restraints excluded: chain K residue 423 LYS Chi-restraints excluded: chain K residue 429 LEU Chi-restraints excluded: chain K residue 446 ARG Chi-restraints excluded: chain K residue 448 GLU Chi-restraints excluded: chain K residue 449 ASP Chi-restraints excluded: chain K residue 453 LEU Chi-restraints excluded: chain K residue 455 LYS Chi-restraints excluded: chain L residue 703 GLN Chi-restraints excluded: chain Z residue 20 LYS Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 80 PHE Chi-restraints excluded: chain Z residue 87 ILE Chi-restraints excluded: chain Z residue 88 LYS Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 116 LYS Chi-restraints excluded: chain Z residue 119 GLU Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 122 LEU Chi-restraints excluded: chain Z residue 125 ILE Chi-restraints excluded: chain Z residue 127 GLN Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 129 LEU Chi-restraints excluded: chain Z residue 130 ASN Chi-restraints excluded: chain Z residue 133 THR Chi-restraints excluded: chain Z residue 134 LYS Chi-restraints excluded: chain Z residue 139 PHE Chi-restraints excluded: chain Z residue 765 ASP Chi-restraints excluded: chain Z residue 766 ASN Chi-restraints excluded: chain Z residue 767 ILE Chi-restraints excluded: chain Z residue 808 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 725 optimal weight: 5.9990 chunk 651 optimal weight: 0.4980 chunk 361 optimal weight: 0.5980 chunk 222 optimal weight: 20.0000 chunk 439 optimal weight: 0.6980 chunk 347 optimal weight: 1.9990 chunk 673 optimal weight: 7.9990 chunk 260 optimal weight: 7.9990 chunk 409 optimal weight: 4.9990 chunk 501 optimal weight: 5.9990 chunk 780 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN C 262 ASN C 476 ASN C1290 ASN D 431 ASN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 484 GLN D 622 GLN ** D 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 ASN D1160 HIS D1493 ASN E 36 GLN E 190 GLN ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 HIS ** E 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 636 GLN E 745 HIS E 759 ASN E 763 GLN E 770 HIS E 822 ASN E 964 GLN E 975 GLN E1001 ASN E1093 ASN E1102 GLN E1306 ASN E1493 ASN E1539 ASN E1558 GLN F 68 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 GLN F 258 GLN ** F 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 686 ASN ** F 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 985 GLN F1240 HIS F1299 ASN F1365 ASN F1619 ASN G 301 HIS G 324 GLN G 328 GLN ** G 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 ASN H 377 ASN H 524 ASN ** I 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 690 GLN I 695 GLN ** I 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 754 ASN I 781 ASN ** J 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 367 ASN J 374 GLN J 378 HIS J 399 ASN J 462 GLN K 351 GLN K 359 ASN K 377 ASN K 387 GLN K 418 GLN ** L 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 695 GLN L 749 GLN ** L 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 19 ASN Z 127 GLN Z 196 ASN Z 221 GLN Z 280 GLN Z 281 GLN ** Z 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 396 GLN Z 424 ASN Z 608 GLN ** Z 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 719 ASN ** Z 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 834 ASN Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4488 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 68075 Z= 0.265 Angle : 0.863 19.517 92300 Z= 0.451 Chirality : 0.048 0.342 10884 Planarity : 0.006 0.174 11817 Dihedral : 9.127 97.402 9515 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.57 % Allowed : 8.81 % Favored : 90.62 % Rotamer: Outliers : 4.30 % Allowed : 13.34 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.05 % Twisted Proline : 0.86 % Twisted General : 0.17 % 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: -1.88 (0.09), residues: 8584 helix: -0.40 (0.07), residues: 5060 sheet: 0.04 (0.26), residues: 375 loop : -2.80 (0.11), residues: 3149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E1495 HIS 0.016 0.002 HIS E1429 PHE 0.045 0.002 PHE E 220 TYR 0.060 0.002 TYR G 387 ARG 0.006 0.001 ARG C1198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 7900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 673 time to evaluate : 5.708 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: A 438 MET cc_start: 0.0180 (pmm) cc_final: -0.0421 (mtt) REVERT: A 501 MET cc_start: 0.2893 (ppp) cc_final: 0.2627 (ppp) REVERT: A 645 GLN cc_start: -0.0449 (OUTLIER) cc_final: -0.0690 (tt0) REVERT: A 819 MET cc_start: -0.0278 (mtp) cc_final: -0.3428 (mmm) REVERT: C 388 MET cc_start: -0.0961 (mmm) cc_final: -0.2235 (ptm) REVERT: C 495 THR cc_start: 0.2515 (m) cc_final: 0.2296 (m) REVERT: C 861 GLN cc_start: 0.5015 (tt0) cc_final: 0.4758 (mm-40) REVERT: C 945 CYS cc_start: 0.7607 (OUTLIER) cc_final: 0.6824 (p) REVERT: C 1104 LYS cc_start: 0.1456 (tttt) cc_final: 0.0808 (mmmm) REVERT: C 1278 ASP cc_start: 0.2652 (p0) cc_final: 0.2104 (m-30) REVERT: C 1289 MET cc_start: 0.1386 (tpp) cc_final: 0.0833 (tpp) REVERT: C 1299 LYS cc_start: 0.3481 (OUTLIER) cc_final: 0.1556 (tptt) REVERT: C 1387 HIS cc_start: 0.4762 (OUTLIER) cc_final: 0.3366 (t-90) REVERT: D 199 ASN cc_start: 0.3571 (m-40) cc_final: 0.2830 (t0) REVERT: D 327 MET cc_start: 0.0960 (mmm) cc_final: 0.0567 (ttt) REVERT: D 669 PHE cc_start: 0.2944 (t80) cc_final: 0.2530 (t80) REVERT: D 1324 ILE cc_start: 0.5956 (mt) cc_final: 0.5449 (mt) REVERT: E 121 ASP cc_start: 0.6404 (m-30) cc_final: 0.5879 (p0) REVERT: E 187 PHE cc_start: 0.6308 (t80) cc_final: 0.5929 (t80) REVERT: E 284 ILE cc_start: 0.7213 (mm) cc_final: 0.6981 (mm) REVERT: E 317 PHE cc_start: 0.7522 (m-80) cc_final: 0.7266 (m-10) REVERT: E 321 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.6831 (tt) REVERT: E 496 LEU cc_start: 0.6816 (pp) cc_final: 0.6522 (pp) REVERT: E 648 ARG cc_start: 0.7029 (mtt90) cc_final: 0.4942 (mtm-85) REVERT: E 771 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.5468 (mt) REVERT: E 808 THR cc_start: 0.8901 (p) cc_final: 0.8651 (p) REVERT: E 878 PHE cc_start: 0.7694 (OUTLIER) cc_final: 0.6559 (m-10) REVERT: E 1123 HIS cc_start: 0.7571 (m-70) cc_final: 0.7124 (t-90) REVERT: E 1469 LEU cc_start: 0.5691 (tt) cc_final: 0.5229 (tt) REVERT: F 68 GLN cc_start: 0.0523 (OUTLIER) cc_final: -0.0226 (mt0) REVERT: F 384 MET cc_start: 0.3877 (ppp) cc_final: 0.3416 (ppp) REVERT: F 533 LEU cc_start: -0.0814 (OUTLIER) cc_final: -0.1347 (mt) REVERT: F 965 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7380 (tp) REVERT: F 1027 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7688 (pt0) REVERT: F 1082 ILE cc_start: 0.8388 (mm) cc_final: 0.8107 (mm) REVERT: F 1097 TYR cc_start: 0.4463 (t80) cc_final: 0.3515 (t80) REVERT: F 1142 GLU cc_start: 0.3770 (OUTLIER) cc_final: 0.1210 (mm-30) REVERT: F 1196 SER cc_start: 0.7462 (t) cc_final: 0.6919 (m) REVERT: F 1243 GLU cc_start: 0.2265 (pt0) cc_final: 0.2005 (pt0) REVERT: F 1373 ASP cc_start: 0.6293 (OUTLIER) cc_final: 0.5264 (t70) REVERT: F 1387 THR cc_start: 0.6768 (OUTLIER) cc_final: 0.6295 (t) REVERT: F 1484 ARG cc_start: 0.6120 (OUTLIER) cc_final: 0.5549 (mmt-90) REVERT: F 1490 ARG cc_start: 0.4915 (mmm-85) cc_final: 0.4640 (mmm-85) REVERT: H 446 ARG cc_start: 0.7550 (ttt180) cc_final: 0.6195 (mmm160) REVERT: H 455 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7250 (tmtt) REVERT: I 678 GLN cc_start: 0.4303 (OUTLIER) cc_final: 0.3246 (tp40) REVERT: I 714 PHE cc_start: 0.1507 (t80) cc_final: 0.1128 (t80) REVERT: I 764 SER cc_start: 0.7553 (m) cc_final: 0.7343 (p) REVERT: I 778 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7555 (tptp) REVERT: J 377 ILE cc_start: 0.5900 (OUTLIER) cc_final: 0.5667 (mt) REVERT: K 404 ARG cc_start: 0.3152 (OUTLIER) cc_final: 0.2501 (ttt90) REVERT: L 695 GLN cc_start: 0.1898 (OUTLIER) cc_final: 0.1674 (pm20) REVERT: L 771 ASN cc_start: 0.6391 (OUTLIER) cc_final: 0.6132 (p0) REVERT: Z 80 PHE cc_start: 0.4521 (OUTLIER) cc_final: 0.4064 (m-80) REVERT: Z 122 LEU cc_start: 0.3679 (OUTLIER) cc_final: 0.2405 (mp) REVERT: Z 139 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7362 (t80) REVERT: Z 399 LYS cc_start: 0.3202 (mptt) cc_final: 0.2922 (mmtp) REVERT: Z 459 LEU cc_start: 0.5986 (tp) cc_final: 0.5700 (tp) REVERT: Z 541 TYR cc_start: 0.7403 (t80) cc_final: 0.7016 (t80) REVERT: Z 573 HIS cc_start: 0.7535 (m-70) cc_final: 0.7274 (m90) REVERT: Z 625 GLU cc_start: 0.6714 (tt0) cc_final: 0.6192 (tt0) REVERT: Z 696 TYR cc_start: 0.6272 (m-10) cc_final: 0.5976 (m-80) REVERT: Z 702 ILE cc_start: 0.2922 (mt) cc_final: 0.2346 (mm) outliers start: 311 outliers final: 149 residues processed: 942 average time/residue: 0.6107 time to fit residues: 1001.6089 Evaluate side-chains 700 residues out of total 7900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 526 time to evaluate : 5.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 896 CYS Chi-restraints excluded: chain C residue 900 ASP Chi-restraints excluded: chain C residue 945 CYS Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 1290 ASN Chi-restraints excluded: chain C residue 1299 LYS Chi-restraints excluded: chain C residue 1301 SER Chi-restraints excluded: chain C residue 1387 HIS Chi-restraints excluded: chain D residue 886 ASN Chi-restraints excluded: chain D residue 1081 CYS Chi-restraints excluded: chain D residue 1304 THR Chi-restraints excluded: chain D residue 1329 ASP Chi-restraints excluded: chain D residue 1343 LEU Chi-restraints excluded: chain D residue 1493 ASN Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 600 ASN Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 699 GLU Chi-restraints excluded: chain E residue 706 THR Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 771 LEU Chi-restraints excluded: chain E residue 773 LEU Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain E residue 878 PHE Chi-restraints excluded: chain E residue 895 HIS Chi-restraints excluded: chain E residue 1012 VAL Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1047 LEU Chi-restraints excluded: chain E residue 1079 VAL Chi-restraints excluded: chain E residue 1197 VAL Chi-restraints excluded: chain E residue 1211 ILE Chi-restraints excluded: chain E residue 1227 VAL Chi-restraints excluded: chain E residue 1238 ILE Chi-restraints excluded: chain E residue 1297 LYS Chi-restraints excluded: chain E residue 1444 LEU Chi-restraints excluded: chain E residue 1466 TYR Chi-restraints excluded: chain E residue 1557 LEU Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 397 MET Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain F residue 533 LEU Chi-restraints excluded: chain F residue 686 ASN Chi-restraints excluded: chain F residue 713 PHE Chi-restraints excluded: chain F residue 716 LEU Chi-restraints excluded: chain F residue 717 ILE Chi-restraints excluded: chain F residue 719 ILE Chi-restraints excluded: chain F residue 750 TRP Chi-restraints excluded: chain F residue 837 TYR Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 926 LEU Chi-restraints excluded: chain F residue 928 LEU Chi-restraints excluded: chain F residue 958 SER Chi-restraints excluded: chain F residue 965 LEU Chi-restraints excluded: chain F residue 1027 GLN Chi-restraints excluded: chain F residue 1032 ILE Chi-restraints excluded: chain F residue 1041 PHE Chi-restraints excluded: chain F residue 1060 LEU Chi-restraints excluded: chain F residue 1068 ILE Chi-restraints excluded: chain F residue 1090 PRO Chi-restraints excluded: chain F residue 1139 ILE Chi-restraints excluded: chain F residue 1142 GLU Chi-restraints excluded: chain F residue 1144 VAL Chi-restraints excluded: chain F residue 1153 TYR Chi-restraints excluded: chain F residue 1161 LEU Chi-restraints excluded: chain F residue 1181 VAL Chi-restraints excluded: chain F residue 1191 SER Chi-restraints excluded: chain F residue 1195 PHE Chi-restraints excluded: chain F residue 1217 THR Chi-restraints excluded: chain F residue 1277 VAL Chi-restraints excluded: chain F residue 1280 ILE Chi-restraints excluded: chain F residue 1285 HIS Chi-restraints excluded: chain F residue 1299 ASN Chi-restraints excluded: chain F residue 1309 LEU Chi-restraints excluded: chain F residue 1313 ILE Chi-restraints excluded: chain F residue 1315 THR Chi-restraints excluded: chain F residue 1372 THR Chi-restraints excluded: chain F residue 1373 ASP Chi-restraints excluded: chain F residue 1387 THR Chi-restraints excluded: chain F residue 1407 ILE Chi-restraints excluded: chain F residue 1417 LEU Chi-restraints excluded: chain F residue 1439 GLU Chi-restraints excluded: chain F residue 1484 ARG Chi-restraints excluded: chain F residue 1624 GLN Chi-restraints excluded: chain F residue 1635 ARG Chi-restraints excluded: chain G residue 303 GLU Chi-restraints excluded: chain G residue 333 ILE Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain I residue 678 GLN Chi-restraints excluded: chain I residue 728 THR Chi-restraints excluded: chain I residue 745 TYR Chi-restraints excluded: chain I residue 778 LYS Chi-restraints excluded: chain I residue 795 LYS Chi-restraints excluded: chain I residue 797 LEU Chi-restraints excluded: chain I residue 810 ASN Chi-restraints excluded: chain I residue 821 ILE Chi-restraints excluded: chain I residue 823 LYS Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 368 ASP Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain J residue 398 VAL Chi-restraints excluded: chain J residue 399 ASN Chi-restraints excluded: chain J residue 411 ASN Chi-restraints excluded: chain K residue 299 TRP Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain K residue 404 ARG Chi-restraints excluded: chain K residue 436 MET Chi-restraints excluded: chain K residue 448 GLU Chi-restraints excluded: chain K residue 449 ASP Chi-restraints excluded: chain K residue 453 LEU Chi-restraints excluded: chain L residue 695 GLN Chi-restraints excluded: chain L residue 771 ASN Chi-restraints excluded: chain L residue 793 LEU Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 80 PHE Chi-restraints excluded: chain Z residue 116 LYS Chi-restraints excluded: chain Z residue 119 GLU Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 122 LEU Chi-restraints excluded: chain Z residue 125 ILE Chi-restraints excluded: chain Z residue 129 LEU Chi-restraints excluded: chain Z residue 134 LYS Chi-restraints excluded: chain Z residue 139 PHE Chi-restraints excluded: chain Z residue 394 TYR Chi-restraints excluded: chain Z residue 589 LEU Chi-restraints excluded: chain Z residue 619 PHE Chi-restraints excluded: chain Z residue 630 ARG Chi-restraints excluded: chain Z residue 637 ILE Chi-restraints excluded: chain Z residue 766 ASN Chi-restraints excluded: chain Z residue 776 ILE Chi-restraints excluded: chain Z residue 793 LYS Chi-restraints excluded: chain Z residue 808 ASN Chi-restraints excluded: chain Z residue 824 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 433 optimal weight: 0.0970 chunk 242 optimal weight: 0.0050 chunk 649 optimal weight: 1.9990 chunk 531 optimal weight: 20.0000 chunk 215 optimal weight: 30.0000 chunk 781 optimal weight: 20.0000 chunk 844 optimal weight: 2.9990 chunk 695 optimal weight: 4.9990 chunk 774 optimal weight: 0.7980 chunk 266 optimal weight: 30.0000 chunk 626 optimal weight: 5.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 914 GLN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 850 ASN ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 GLN ** E 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 600 ASN E 710 GLN E 792 GLN E 983 ASN F 68 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 GLN ** F 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 714 HIS F 758 ASN ** F 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 893 HIS ** F 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1299 ASN ** G 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 365 GLN H 385 GLN H 418 GLN ** I 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 462 GLN K 418 GLN ** L 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 695 GLN L 749 GLN ** L 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 380 HIS ** Z 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 464 ASN ** Z 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4468 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 68075 Z= 0.216 Angle : 0.762 15.750 92300 Z= 0.397 Chirality : 0.045 0.350 10884 Planarity : 0.005 0.165 11817 Dihedral : 7.662 88.935 9323 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.80 % Favored : 90.76 % Rotamer: Outliers : 3.84 % Allowed : 15.92 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.05 % Twisted Proline : 0.86 % Twisted General : 0.07 % 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: -1.34 (0.09), residues: 8584 helix: 0.10 (0.07), residues: 5056 sheet: 0.16 (0.27), residues: 371 loop : -2.69 (0.11), residues: 3157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D1450 HIS 0.015 0.001 HIS E1429 PHE 0.038 0.002 PHE F1474 TYR 0.056 0.002 TYR G 387 ARG 0.011 0.001 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 7900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 615 time to evaluate : 7.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.0615 (OUTLIER) cc_final: -0.0049 (ttmm) REVERT: A 438 MET cc_start: -0.0252 (OUTLIER) cc_final: -0.0498 (mtt) REVERT: A 501 MET cc_start: 0.3188 (ppp) cc_final: 0.2950 (ppp) REVERT: A 819 MET cc_start: -0.0434 (mtp) cc_final: -0.3544 (mmm) REVERT: C 117 TYR cc_start: -0.0348 (OUTLIER) cc_final: -0.1336 (p90) REVERT: C 388 MET cc_start: -0.0557 (mmm) cc_final: -0.2022 (ptm) REVERT: C 861 GLN cc_start: 0.5157 (tt0) cc_final: 0.4825 (mm-40) REVERT: C 945 CYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6678 (p) REVERT: C 982 GLU cc_start: 0.4323 (mt-10) cc_final: 0.3721 (pp20) REVERT: C 1104 LYS cc_start: 0.1693 (tttt) cc_final: 0.1115 (mmmm) REVERT: C 1278 ASP cc_start: 0.2944 (p0) cc_final: 0.2624 (m-30) REVERT: C 1387 HIS cc_start: 0.4871 (OUTLIER) cc_final: 0.3894 (t70) REVERT: D 199 ASN cc_start: 0.3527 (m-40) cc_final: 0.2774 (t0) REVERT: D 327 MET cc_start: 0.0956 (mmm) cc_final: 0.0544 (ttt) REVERT: E 121 ASP cc_start: 0.6330 (m-30) cc_final: 0.5906 (p0) REVERT: E 321 ILE cc_start: 0.7343 (OUTLIER) cc_final: 0.6891 (tt) REVERT: E 771 LEU cc_start: 0.6155 (OUTLIER) cc_final: 0.5529 (mt) REVERT: E 808 THR cc_start: 0.8823 (p) cc_final: 0.8576 (p) REVERT: E 1123 HIS cc_start: 0.7621 (m-70) cc_final: 0.7132 (t-90) REVERT: E 1469 LEU cc_start: 0.5730 (tt) cc_final: 0.5317 (tt) REVERT: F 384 MET cc_start: 0.3480 (ppp) cc_final: 0.3048 (ppp) REVERT: F 533 LEU cc_start: -0.0664 (OUTLIER) cc_final: -0.0925 (mt) REVERT: F 965 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7465 (tp) REVERT: F 1027 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7694 (pt0) REVERT: F 1082 ILE cc_start: 0.8319 (mm) cc_final: 0.8023 (mm) REVERT: F 1142 GLU cc_start: 0.3480 (OUTLIER) cc_final: 0.1672 (mm-30) REVERT: F 1196 SER cc_start: 0.7388 (t) cc_final: 0.6841 (m) REVERT: F 1373 ASP cc_start: 0.6196 (OUTLIER) cc_final: 0.5501 (t70) REVERT: F 1387 THR cc_start: 0.6937 (OUTLIER) cc_final: 0.6654 (t) REVERT: H 385 GLN cc_start: 0.7013 (mt0) cc_final: 0.6706 (mt0) REVERT: H 446 ARG cc_start: 0.7624 (ttt180) cc_final: 0.6437 (mmm160) REVERT: I 678 GLN cc_start: 0.4766 (OUTLIER) cc_final: 0.3500 (tp-100) REVERT: I 795 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7239 (mtmt) REVERT: J 303 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6879 (pm20) REVERT: J 377 ILE cc_start: 0.5824 (OUTLIER) cc_final: 0.5585 (mt) REVERT: K 404 ARG cc_start: 0.3070 (OUTLIER) cc_final: 0.2558 (ttm-80) REVERT: K 469 ARG cc_start: 0.5616 (mmp80) cc_final: 0.5280 (mpt180) REVERT: L 771 ASN cc_start: 0.6008 (OUTLIER) cc_final: 0.5687 (p0) REVERT: Z 80 PHE cc_start: 0.4704 (OUTLIER) cc_final: 0.4274 (m-80) REVERT: Z 122 LEU cc_start: 0.4156 (OUTLIER) cc_final: 0.2877 (mp) REVERT: Z 139 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7491 (t80) REVERT: Z 399 LYS cc_start: 0.3430 (mptt) cc_final: 0.3005 (mmtp) REVERT: Z 459 LEU cc_start: 0.5454 (tp) cc_final: 0.4907 (tt) REVERT: Z 541 TYR cc_start: 0.7352 (t80) cc_final: 0.6873 (t80) REVERT: Z 625 GLU cc_start: 0.6700 (tt0) cc_final: 0.6249 (tt0) REVERT: Z 696 TYR cc_start: 0.6129 (m-10) cc_final: 0.5740 (m-80) REVERT: Z 702 ILE cc_start: 0.2957 (mt) cc_final: 0.2360 (mm) outliers start: 278 outliers final: 139 residues processed: 842 average time/residue: 0.6337 time to fit residues: 937.9069 Evaluate side-chains 667 residues out of total 7900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 506 time to evaluate : 5.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 438 MET Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 900 ASP Chi-restraints excluded: chain C residue 945 CYS Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 1013 LYS Chi-restraints excluded: chain C residue 1387 HIS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 1301 ILE Chi-restraints excluded: chain D residue 1304 THR Chi-restraints excluded: chain D residue 1329 ASP Chi-restraints excluded: chain D residue 1343 LEU Chi-restraints excluded: chain D residue 1416 PHE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 435 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 600 ASN Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 694 ILE Chi-restraints excluded: chain E residue 699 GLU Chi-restraints excluded: chain E residue 706 THR Chi-restraints excluded: chain E residue 708 THR Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 771 LEU Chi-restraints excluded: chain E residue 773 LEU Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain E residue 830 THR Chi-restraints excluded: chain E residue 895 HIS Chi-restraints excluded: chain E residue 909 GLU Chi-restraints excluded: chain E residue 1008 THR Chi-restraints excluded: chain E residue 1012 VAL Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1047 LEU Chi-restraints excluded: chain E residue 1079 VAL Chi-restraints excluded: chain E residue 1211 ILE Chi-restraints excluded: chain E residue 1227 VAL Chi-restraints excluded: chain E residue 1238 ILE Chi-restraints excluded: chain E residue 1262 LEU Chi-restraints excluded: chain E residue 1340 PHE Chi-restraints excluded: chain E residue 1466 TYR Chi-restraints excluded: chain E residue 1514 VAL Chi-restraints excluded: chain E residue 1557 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain F residue 533 LEU Chi-restraints excluded: chain F residue 565 TYR Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 713 PHE Chi-restraints excluded: chain F residue 719 ILE Chi-restraints excluded: chain F residue 781 LEU Chi-restraints excluded: chain F residue 837 TYR Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 926 LEU Chi-restraints excluded: chain F residue 928 LEU Chi-restraints excluded: chain F residue 958 SER Chi-restraints excluded: chain F residue 965 LEU Chi-restraints excluded: chain F residue 982 PHE Chi-restraints excluded: chain F residue 1027 GLN Chi-restraints excluded: chain F residue 1041 PHE Chi-restraints excluded: chain F residue 1056 LEU Chi-restraints excluded: chain F residue 1128 ASP Chi-restraints excluded: chain F residue 1139 ILE Chi-restraints excluded: chain F residue 1142 GLU Chi-restraints excluded: chain F residue 1144 VAL Chi-restraints excluded: chain F residue 1153 TYR Chi-restraints excluded: chain F residue 1181 VAL Chi-restraints excluded: chain F residue 1191 SER Chi-restraints excluded: chain F residue 1195 PHE Chi-restraints excluded: chain F residue 1299 ASN Chi-restraints excluded: chain F residue 1309 LEU Chi-restraints excluded: chain F residue 1313 ILE Chi-restraints excluded: chain F residue 1315 THR Chi-restraints excluded: chain F residue 1360 LEU Chi-restraints excluded: chain F residue 1372 THR Chi-restraints excluded: chain F residue 1373 ASP Chi-restraints excluded: chain F residue 1387 THR Chi-restraints excluded: chain F residue 1407 ILE Chi-restraints excluded: chain F residue 1439 GLU Chi-restraints excluded: chain F residue 1503 THR Chi-restraints excluded: chain F residue 1528 VAL Chi-restraints excluded: chain F residue 1624 GLN Chi-restraints excluded: chain F residue 1629 LEU Chi-restraints excluded: chain F residue 1635 ARG Chi-restraints excluded: chain F residue 1636 LEU Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 380 TYR Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain H residue 465 ILE Chi-restraints excluded: chain I residue 678 GLN Chi-restraints excluded: chain I residue 728 THR Chi-restraints excluded: chain I residue 745 TYR Chi-restraints excluded: chain I residue 795 LYS Chi-restraints excluded: chain I residue 821 ILE Chi-restraints excluded: chain I residue 823 LYS Chi-restraints excluded: chain J residue 303 GLU Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 368 ASP Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 377 ILE Chi-restraints excluded: chain J residue 411 ASN Chi-restraints excluded: chain K residue 299 TRP Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 404 ARG Chi-restraints excluded: chain K residue 448 GLU Chi-restraints excluded: chain K residue 449 ASP Chi-restraints excluded: chain L residue 771 ASN Chi-restraints excluded: chain L residue 793 LEU Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 80 PHE Chi-restraints excluded: chain Z residue 84 ASP Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 116 LYS Chi-restraints excluded: chain Z residue 119 GLU Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 122 LEU Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 129 LEU Chi-restraints excluded: chain Z residue 134 LYS Chi-restraints excluded: chain Z residue 139 PHE Chi-restraints excluded: chain Z residue 394 TYR Chi-restraints excluded: chain Z residue 409 LEU Chi-restraints excluded: chain Z residue 589 LEU Chi-restraints excluded: chain Z residue 630 ARG Chi-restraints excluded: chain Z residue 637 ILE Chi-restraints excluded: chain Z residue 776 ILE Chi-restraints excluded: chain Z residue 793 LYS Chi-restraints excluded: chain Z residue 808 ASN Chi-restraints excluded: chain Z residue 824 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 772 optimal weight: 1.9990 chunk 587 optimal weight: 30.0000 chunk 405 optimal weight: 1.9990 chunk 86 optimal weight: 0.0870 chunk 372 optimal weight: 3.9990 chunk 524 optimal weight: 7.9990 chunk 784 optimal weight: 8.9990 chunk 830 optimal weight: 0.9980 chunk 409 optimal weight: 0.5980 chunk 743 optimal weight: 9.9990 chunk 223 optimal weight: 8.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1049 ASN C1290 ASN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 600 ASN E 804 GLN E1613 ASN ** F 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 GLN ** F 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN ** I 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 359 ASN K 418 GLN L 695 GLN ** L 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 749 GLN ** L 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 817 GLN Z 227 GLN ** Z 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 391 HIS Z 563 ASN ** Z 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4473 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 68075 Z= 0.206 Angle : 0.725 15.977 92300 Z= 0.374 Chirality : 0.044 0.337 10884 Planarity : 0.005 0.159 11817 Dihedral : 7.000 82.977 9268 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.43 % Favored : 91.19 % Rotamer: Outliers : 3.86 % Allowed : 16.92 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.05 % Twisted Proline : 0.86 % 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: -1.04 (0.09), residues: 8584 helix: 0.37 (0.07), residues: 5078 sheet: 0.20 (0.27), residues: 377 loop : -2.62 (0.11), residues: 3129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D1450 HIS 0.012 0.001 HIS E1429 PHE 0.031 0.002 PHE F 791 TYR 0.054 0.002 TYR G 387 ARG 0.012 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 7900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 559 time to evaluate : 5.748 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 438 MET cc_start: -0.0250 (pmm) cc_final: -0.0476 (mtt) REVERT: A 501 MET cc_start: 0.3319 (ppp) cc_final: 0.3038 (ppp) REVERT: A 819 MET cc_start: -0.0771 (mtp) cc_final: -0.3701 (mmm) REVERT: C 117 TYR cc_start: -0.0365 (OUTLIER) cc_final: -0.1288 (p90) REVERT: C 388 MET cc_start: -0.0511 (mmm) cc_final: -0.2043 (ptm) REVERT: C 861 GLN cc_start: 0.5196 (tt0) cc_final: 0.4816 (mm-40) REVERT: C 945 CYS cc_start: 0.7413 (OUTLIER) cc_final: 0.6655 (p) REVERT: C 982 GLU cc_start: 0.4337 (mt-10) cc_final: 0.3837 (pp20) REVERT: C 1048 MET cc_start: 0.1216 (mmm) cc_final: 0.0124 (mmm) REVERT: C 1104 LYS cc_start: 0.1904 (tttt) cc_final: 0.1246 (mmmm) REVERT: C 1289 MET cc_start: 0.1526 (tpp) cc_final: 0.0713 (tpp) REVERT: C 1387 HIS cc_start: 0.4753 (OUTLIER) cc_final: 0.3918 (t70) REVERT: D 199 ASN cc_start: 0.3536 (m-40) cc_final: 0.2756 (t0) REVERT: D 207 MET cc_start: 0.2123 (mmt) cc_final: 0.1015 (mmm) REVERT: D 327 MET cc_start: 0.0948 (mmm) cc_final: 0.0553 (ttt) REVERT: D 586 LEU cc_start: -0.0739 (OUTLIER) cc_final: -0.1207 (tt) REVERT: E 121 ASP cc_start: 0.6175 (m-30) cc_final: 0.5840 (p0) REVERT: E 321 ILE cc_start: 0.7395 (OUTLIER) cc_final: 0.6966 (tt) REVERT: E 457 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.5644 (mp) REVERT: E 771 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5580 (mt) REVERT: E 808 THR cc_start: 0.8635 (p) cc_final: 0.8329 (p) REVERT: E 878 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.6833 (m-10) REVERT: E 894 VAL cc_start: 0.7652 (OUTLIER) cc_final: 0.7451 (m) REVERT: E 1460 LEU cc_start: 0.5655 (OUTLIER) cc_final: 0.5411 (mm) REVERT: E 1469 LEU cc_start: 0.5596 (tt) cc_final: 0.4912 (tt) REVERT: F 185 PHE cc_start: 0.3164 (t80) cc_final: 0.2553 (t80) REVERT: F 384 MET cc_start: 0.3216 (ppp) cc_final: 0.2962 (ppp) REVERT: F 397 MET cc_start: 0.6355 (pmm) cc_final: 0.5992 (pmm) REVERT: F 533 LEU cc_start: -0.0350 (OUTLIER) cc_final: -0.0596 (mt) REVERT: F 845 ASP cc_start: 0.7580 (t0) cc_final: 0.7208 (t70) REVERT: F 1082 ILE cc_start: 0.8223 (mm) cc_final: 0.7983 (mm) REVERT: F 1097 TYR cc_start: 0.4232 (t80) cc_final: 0.3944 (t80) REVERT: F 1138 PHE cc_start: 0.5351 (OUTLIER) cc_final: 0.4520 (t80) REVERT: F 1142 GLU cc_start: 0.3508 (OUTLIER) cc_final: 0.2082 (mm-30) REVERT: F 1196 SER cc_start: 0.7456 (t) cc_final: 0.6843 (m) REVERT: F 1373 ASP cc_start: 0.6261 (OUTLIER) cc_final: 0.4229 (m-30) REVERT: F 1387 THR cc_start: 0.7050 (OUTLIER) cc_final: 0.6847 (t) REVERT: G 451 MET cc_start: 0.8267 (ppp) cc_final: 0.8059 (ppp) REVERT: H 375 ILE cc_start: 0.5191 (mt) cc_final: 0.4921 (mt) REVERT: H 378 HIS cc_start: 0.6173 (t-90) cc_final: 0.5937 (t-170) REVERT: H 398 ILE cc_start: 0.6533 (OUTLIER) cc_final: 0.6327 (mt) REVERT: H 446 ARG cc_start: 0.7258 (ttt180) cc_final: 0.6714 (tpp-160) REVERT: I 678 GLN cc_start: 0.4690 (OUTLIER) cc_final: 0.3497 (tp-100) REVERT: I 795 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7383 (mtpt) REVERT: J 386 ASP cc_start: 0.6575 (m-30) cc_final: 0.6369 (m-30) REVERT: J 444 ILE cc_start: 0.5665 (OUTLIER) cc_final: 0.5124 (tp) REVERT: K 404 ARG cc_start: 0.3083 (OUTLIER) cc_final: 0.2552 (ttm-80) REVERT: K 469 ARG cc_start: 0.5352 (mmp80) cc_final: 0.4473 (mmp80) REVERT: L 771 ASN cc_start: 0.6054 (OUTLIER) cc_final: 0.5733 (p0) REVERT: L 773 SER cc_start: 0.5648 (OUTLIER) cc_final: 0.5395 (p) REVERT: Z 80 PHE cc_start: 0.4609 (OUTLIER) cc_final: 0.4236 (m-80) REVERT: Z 122 LEU cc_start: 0.4147 (OUTLIER) cc_final: 0.3073 (mp) REVERT: Z 139 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7295 (t80) REVERT: Z 399 LYS cc_start: 0.3467 (mptt) cc_final: 0.3058 (mmtp) REVERT: Z 459 LEU cc_start: 0.5544 (tp) cc_final: 0.5078 (tt) REVERT: Z 541 TYR cc_start: 0.7476 (t80) cc_final: 0.7138 (t80) REVERT: Z 568 ASP cc_start: 0.7192 (t0) cc_final: 0.6078 (p0) REVERT: Z 625 GLU cc_start: 0.6646 (tt0) cc_final: 0.6206 (tt0) REVERT: Z 661 LEU cc_start: 0.8367 (mt) cc_final: 0.8099 (mt) REVERT: Z 696 TYR cc_start: 0.6015 (m-10) cc_final: 0.5774 (m-80) outliers start: 279 outliers final: 161 residues processed: 797 average time/residue: 0.5978 time to fit residues: 845.1674 Evaluate side-chains 681 residues out of total 7900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 495 time to evaluate : 5.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 822 TYR Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 900 ASP Chi-restraints excluded: chain C residue 945 CYS Chi-restraints excluded: chain C residue 1013 LYS Chi-restraints excluded: chain C residue 1290 ASN Chi-restraints excluded: chain C residue 1347 ILE Chi-restraints excluded: chain C residue 1387 HIS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 783 ASP Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 1301 ILE Chi-restraints excluded: chain D residue 1304 THR Chi-restraints excluded: chain D residue 1329 ASP Chi-restraints excluded: chain D residue 1381 SER Chi-restraints excluded: chain D residue 1384 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 435 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 600 ASN Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 694 ILE Chi-restraints excluded: chain E residue 699 GLU Chi-restraints excluded: chain E residue 706 THR Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 771 LEU Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain E residue 795 ILE Chi-restraints excluded: chain E residue 826 SER Chi-restraints excluded: chain E residue 830 THR Chi-restraints excluded: chain E residue 848 MET Chi-restraints excluded: chain E residue 878 PHE Chi-restraints excluded: chain E residue 894 VAL Chi-restraints excluded: chain E residue 895 HIS Chi-restraints excluded: chain E residue 909 GLU Chi-restraints excluded: chain E residue 1012 VAL Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1047 LEU Chi-restraints excluded: chain E residue 1079 VAL Chi-restraints excluded: chain E residue 1197 VAL Chi-restraints excluded: chain E residue 1201 ILE Chi-restraints excluded: chain E residue 1211 ILE Chi-restraints excluded: chain E residue 1227 VAL Chi-restraints excluded: chain E residue 1238 ILE Chi-restraints excluded: chain E residue 1262 LEU Chi-restraints excluded: chain E residue 1316 LEU Chi-restraints excluded: chain E residue 1340 PHE Chi-restraints excluded: chain E residue 1357 CYS Chi-restraints excluded: chain E residue 1460 LEU Chi-restraints excluded: chain E residue 1466 TYR Chi-restraints excluded: chain E residue 1514 VAL Chi-restraints excluded: chain E residue 1557 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain F residue 533 LEU Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 717 ILE Chi-restraints excluded: chain F residue 719 ILE Chi-restraints excluded: chain F residue 781 LEU Chi-restraints excluded: chain F residue 837 TYR Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 926 LEU Chi-restraints excluded: chain F residue 928 LEU Chi-restraints excluded: chain F residue 936 ILE Chi-restraints excluded: chain F residue 958 SER Chi-restraints excluded: chain F residue 982 PHE Chi-restraints excluded: chain F residue 998 LEU Chi-restraints excluded: chain F residue 1000 LEU Chi-restraints excluded: chain F residue 1041 PHE Chi-restraints excluded: chain F residue 1056 LEU Chi-restraints excluded: chain F residue 1068 ILE Chi-restraints excluded: chain F residue 1128 ASP Chi-restraints excluded: chain F residue 1138 PHE Chi-restraints excluded: chain F residue 1139 ILE Chi-restraints excluded: chain F residue 1142 GLU Chi-restraints excluded: chain F residue 1144 VAL Chi-restraints excluded: chain F residue 1153 TYR Chi-restraints excluded: chain F residue 1161 LEU Chi-restraints excluded: chain F residue 1181 VAL Chi-restraints excluded: chain F residue 1191 SER Chi-restraints excluded: chain F residue 1195 PHE Chi-restraints excluded: chain F residue 1219 VAL Chi-restraints excluded: chain F residue 1309 LEU Chi-restraints excluded: chain F residue 1313 ILE Chi-restraints excluded: chain F residue 1315 THR Chi-restraints excluded: chain F residue 1347 ILE Chi-restraints excluded: chain F residue 1372 THR Chi-restraints excluded: chain F residue 1373 ASP Chi-restraints excluded: chain F residue 1387 THR Chi-restraints excluded: chain F residue 1407 ILE Chi-restraints excluded: chain F residue 1439 GLU Chi-restraints excluded: chain F residue 1472 GLU Chi-restraints excluded: chain F residue 1503 THR Chi-restraints excluded: chain F residue 1528 VAL Chi-restraints excluded: chain F residue 1539 ILE Chi-restraints excluded: chain F residue 1624 GLN Chi-restraints excluded: chain F residue 1636 LEU Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 380 TYR Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain H residue 398 ILE Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain I residue 678 GLN Chi-restraints excluded: chain I residue 745 TYR Chi-restraints excluded: chain I residue 764 SER Chi-restraints excluded: chain I residue 795 LYS Chi-restraints excluded: chain I residue 821 ILE Chi-restraints excluded: chain I residue 823 LYS Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 368 ASP Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 411 ASN Chi-restraints excluded: chain J residue 415 THR Chi-restraints excluded: chain J residue 444 ILE Chi-restraints excluded: chain J residue 461 HIS Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 404 ARG Chi-restraints excluded: chain K residue 448 GLU Chi-restraints excluded: chain L residue 745 TYR Chi-restraints excluded: chain L residue 750 THR Chi-restraints excluded: chain L residue 771 ASN Chi-restraints excluded: chain L residue 773 SER Chi-restraints excluded: chain L residue 793 LEU Chi-restraints excluded: chain Z residue 16 LYS Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 80 PHE Chi-restraints excluded: chain Z residue 84 ASP Chi-restraints excluded: chain Z residue 116 LYS Chi-restraints excluded: chain Z residue 119 GLU Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 122 LEU Chi-restraints excluded: chain Z residue 129 LEU Chi-restraints excluded: chain Z residue 134 LYS Chi-restraints excluded: chain Z residue 139 PHE Chi-restraints excluded: chain Z residue 388 THR Chi-restraints excluded: chain Z residue 394 TYR Chi-restraints excluded: chain Z residue 409 LEU Chi-restraints excluded: chain Z residue 514 LYS Chi-restraints excluded: chain Z residue 589 LEU Chi-restraints excluded: chain Z residue 630 ARG Chi-restraints excluded: chain Z residue 637 ILE Chi-restraints excluded: chain Z residue 716 LEU Chi-restraints excluded: chain Z residue 776 ILE Chi-restraints excluded: chain Z residue 793 LYS Chi-restraints excluded: chain Z residue 804 ASP Chi-restraints excluded: chain Z residue 808 ASN Chi-restraints excluded: chain Z residue 824 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 691 optimal weight: 7.9990 chunk 471 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 618 optimal weight: 1.9990 chunk 342 optimal weight: 1.9990 chunk 708 optimal weight: 0.9980 chunk 573 optimal weight: 0.7980 chunk 0 optimal weight: 50.0000 chunk 423 optimal weight: 0.9980 chunk 745 optimal weight: 50.0000 chunk 209 optimal weight: 20.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 GLN ** C1290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 600 ASN E1492 HIS ** E1613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN F 160 GLN F 161 GLN ** F 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 506 ASN ** F 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 861 GLN F 985 GLN F1244 ASN F1465 GLN I 657 GLN ** I 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 800 HIS ** J 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 418 GLN L 695 GLN ** L 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4455 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 68075 Z= 0.189 Angle : 0.701 17.226 92300 Z= 0.361 Chirality : 0.043 0.315 10884 Planarity : 0.005 0.155 11817 Dihedral : 6.577 78.595 9249 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.48 % Favored : 91.18 % Rotamer: Outliers : 3.62 % Allowed : 17.54 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.05 % Twisted Proline : 0.86 % Twisted General : 0.04 % 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: -0.81 (0.09), residues: 8584 helix: 0.56 (0.07), residues: 5086 sheet: 0.23 (0.27), residues: 379 loop : -2.55 (0.11), residues: 3119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E1495 HIS 0.011 0.001 HIS E1429 PHE 0.055 0.002 PHE F 572 TYR 0.054 0.001 TYR G 387 ARG 0.007 0.000 ARG D1254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 7900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 558 time to evaluate : 6.031 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 57 ARG cc_start: 0.4258 (mtm180) cc_final: 0.4022 (mpp80) REVERT: A 501 MET cc_start: 0.3341 (ppp) cc_final: 0.3094 (ppp) REVERT: A 819 MET cc_start: -0.0971 (mtp) cc_final: -0.3816 (mmm) REVERT: C 117 TYR cc_start: -0.0435 (OUTLIER) cc_final: -0.1333 (p90) REVERT: C 388 MET cc_start: -0.0464 (mmm) cc_final: -0.2006 (ptm) REVERT: C 487 LYS cc_start: 0.2146 (tptm) cc_final: 0.1260 (ttpt) REVERT: C 861 GLN cc_start: 0.5173 (tt0) cc_final: 0.4762 (mm-40) REVERT: C 945 CYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6624 (p) REVERT: C 982 GLU cc_start: 0.4305 (mt-10) cc_final: 0.3863 (pp20) REVERT: C 1048 MET cc_start: 0.1231 (mmm) cc_final: 0.0207 (mmm) REVERT: C 1104 LYS cc_start: 0.1938 (tttt) cc_final: 0.1482 (mmtp) REVERT: C 1289 MET cc_start: 0.1203 (tpp) cc_final: 0.0391 (tpp) REVERT: C 1387 HIS cc_start: 0.4783 (OUTLIER) cc_final: 0.4051 (t70) REVERT: D 199 ASN cc_start: 0.3545 (m-40) cc_final: 0.2714 (t0) REVERT: D 207 MET cc_start: 0.2127 (mmt) cc_final: 0.0944 (mmm) REVERT: D 327 MET cc_start: 0.1032 (mmm) cc_final: 0.0651 (ttt) REVERT: D 586 LEU cc_start: -0.0754 (OUTLIER) cc_final: -0.1230 (tt) REVERT: E 121 ASP cc_start: 0.6140 (m-30) cc_final: 0.5850 (p0) REVERT: E 321 ILE cc_start: 0.7341 (OUTLIER) cc_final: 0.6976 (tt) REVERT: E 457 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.5687 (mp) REVERT: E 648 ARG cc_start: 0.7034 (mtt90) cc_final: 0.6198 (ptp-170) REVERT: E 669 LEU cc_start: 0.5616 (OUTLIER) cc_final: 0.5294 (tt) REVERT: E 771 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5609 (mt) REVERT: E 781 ASP cc_start: 0.7054 (OUTLIER) cc_final: 0.6716 (t0) REVERT: E 808 THR cc_start: 0.8487 (p) cc_final: 0.8205 (p) REVERT: E 878 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.6940 (m-10) REVERT: E 1167 LEU cc_start: 0.8583 (mm) cc_final: 0.8347 (mm) REVERT: E 1210 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6751 (tp) REVERT: E 1460 LEU cc_start: 0.5503 (OUTLIER) cc_final: 0.5295 (mm) REVERT: E 1469 LEU cc_start: 0.5625 (tt) cc_final: 0.4943 (tt) REVERT: F 533 LEU cc_start: 0.0392 (OUTLIER) cc_final: -0.0039 (mt) REVERT: F 730 VAL cc_start: 0.3691 (OUTLIER) cc_final: 0.3143 (t) REVERT: F 845 ASP cc_start: 0.7441 (t0) cc_final: 0.7037 (t70) REVERT: F 1056 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.5337 (tp) REVERT: F 1082 ILE cc_start: 0.8153 (mm) cc_final: 0.7938 (mm) REVERT: F 1138 PHE cc_start: 0.5493 (OUTLIER) cc_final: 0.4796 (t80) REVERT: F 1196 SER cc_start: 0.7397 (t) cc_final: 0.6779 (m) REVERT: F 1373 ASP cc_start: 0.6099 (OUTLIER) cc_final: 0.5139 (t70) REVERT: G 381 GLU cc_start: 0.8600 (tp30) cc_final: 0.8380 (tp30) REVERT: H 375 ILE cc_start: 0.5226 (mt) cc_final: 0.4986 (mt) REVERT: H 378 HIS cc_start: 0.6141 (t-90) cc_final: 0.5700 (t-170) REVERT: H 436 MET cc_start: 0.6349 (mmt) cc_final: 0.5833 (mmm) REVERT: H 446 ARG cc_start: 0.7466 (ttt180) cc_final: 0.6896 (tpp-160) REVERT: I 647 GLN cc_start: 0.3610 (OUTLIER) cc_final: 0.3070 (mt0) REVERT: I 678 GLN cc_start: 0.4531 (OUTLIER) cc_final: 0.3399 (tp-100) REVERT: I 690 GLN cc_start: -0.0523 (OUTLIER) cc_final: -0.1005 (mm-40) REVERT: J 386 ASP cc_start: 0.6481 (m-30) cc_final: 0.6280 (m-30) REVERT: J 444 ILE cc_start: 0.5860 (OUTLIER) cc_final: 0.5322 (tp) REVERT: J 463 LYS cc_start: 0.6729 (mmpt) cc_final: 0.6188 (mtmm) REVERT: K 404 ARG cc_start: 0.3270 (OUTLIER) cc_final: 0.2200 (ttm-80) REVERT: K 469 ARG cc_start: 0.5492 (mmp80) cc_final: 0.4962 (mmt-90) REVERT: L 749 GLN cc_start: 0.4101 (mm-40) cc_final: 0.3776 (tp40) REVERT: L 771 ASN cc_start: 0.6117 (OUTLIER) cc_final: 0.5810 (p0) REVERT: L 823 LYS cc_start: 0.2841 (mtmm) cc_final: 0.2180 (pttp) REVERT: Z 80 PHE cc_start: 0.4613 (OUTLIER) cc_final: 0.4355 (m-80) REVERT: Z 122 LEU cc_start: 0.4055 (OUTLIER) cc_final: 0.2808 (pp) REVERT: Z 139 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7528 (t80) REVERT: Z 294 MET cc_start: 0.1831 (tmm) cc_final: 0.1526 (tpt) REVERT: Z 399 LYS cc_start: 0.3486 (mptt) cc_final: 0.3072 (mmtp) REVERT: Z 459 LEU cc_start: 0.5386 (tp) cc_final: 0.4896 (tt) REVERT: Z 568 ASP cc_start: 0.7333 (t0) cc_final: 0.6170 (p0) REVERT: Z 625 GLU cc_start: 0.6779 (tt0) cc_final: 0.6295 (tt0) REVERT: Z 661 LEU cc_start: 0.8252 (mt) cc_final: 0.7986 (mt) REVERT: Z 702 ILE cc_start: 0.2601 (mt) cc_final: 0.2338 (mm) outliers start: 262 outliers final: 157 residues processed: 783 average time/residue: 0.6039 time to fit residues: 835.1860 Evaluate side-chains 676 residues out of total 7900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 493 time to evaluate : 5.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 900 ASP Chi-restraints excluded: chain C residue 945 CYS Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 1013 LYS Chi-restraints excluded: chain C residue 1347 ILE Chi-restraints excluded: chain C residue 1387 HIS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 500 MET Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 783 ASP Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 980 SER Chi-restraints excluded: chain D residue 1161 MET Chi-restraints excluded: chain D residue 1301 ILE Chi-restraints excluded: chain D residue 1304 THR Chi-restraints excluded: chain D residue 1329 ASP Chi-restraints excluded: chain D residue 1381 SER Chi-restraints excluded: chain D residue 1384 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 303 GLU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 602 VAL Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 699 GLU Chi-restraints excluded: chain E residue 706 THR Chi-restraints excluded: chain E residue 717 VAL Chi-restraints excluded: chain E residue 753 TYR Chi-restraints excluded: chain E residue 771 LEU Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain E residue 781 ASP Chi-restraints excluded: chain E residue 795 ILE Chi-restraints excluded: chain E residue 826 SER Chi-restraints excluded: chain E residue 830 THR Chi-restraints excluded: chain E residue 848 MET Chi-restraints excluded: chain E residue 878 PHE Chi-restraints excluded: chain E residue 895 HIS Chi-restraints excluded: chain E residue 900 ILE Chi-restraints excluded: chain E residue 909 GLU Chi-restraints excluded: chain E residue 982 ILE Chi-restraints excluded: chain E residue 1012 VAL Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1028 THR Chi-restraints excluded: chain E residue 1079 VAL Chi-restraints excluded: chain E residue 1210 LEU Chi-restraints excluded: chain E residue 1211 ILE Chi-restraints excluded: chain E residue 1227 VAL Chi-restraints excluded: chain E residue 1238 ILE Chi-restraints excluded: chain E residue 1262 LEU Chi-restraints excluded: chain E residue 1316 LEU Chi-restraints excluded: chain E residue 1357 CYS Chi-restraints excluded: chain E residue 1453 ILE Chi-restraints excluded: chain E residue 1460 LEU Chi-restraints excluded: chain E residue 1466 TYR Chi-restraints excluded: chain E residue 1514 VAL Chi-restraints excluded: chain E residue 1557 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 533 LEU Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 713 PHE Chi-restraints excluded: chain F residue 717 ILE Chi-restraints excluded: chain F residue 719 ILE Chi-restraints excluded: chain F residue 730 VAL Chi-restraints excluded: chain F residue 827 ILE Chi-restraints excluded: chain F residue 837 TYR Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 926 LEU Chi-restraints excluded: chain F residue 928 LEU Chi-restraints excluded: chain F residue 936 ILE Chi-restraints excluded: chain F residue 965 LEU Chi-restraints excluded: chain F residue 982 PHE Chi-restraints excluded: chain F residue 985 GLN Chi-restraints excluded: chain F residue 998 LEU Chi-restraints excluded: chain F residue 1056 LEU Chi-restraints excluded: chain F residue 1128 ASP Chi-restraints excluded: chain F residue 1138 PHE Chi-restraints excluded: chain F residue 1139 ILE Chi-restraints excluded: chain F residue 1144 VAL Chi-restraints excluded: chain F residue 1153 TYR Chi-restraints excluded: chain F residue 1181 VAL Chi-restraints excluded: chain F residue 1191 SER Chi-restraints excluded: chain F residue 1195 PHE Chi-restraints excluded: chain F residue 1219 VAL Chi-restraints excluded: chain F residue 1313 ILE Chi-restraints excluded: chain F residue 1315 THR Chi-restraints excluded: chain F residue 1347 ILE Chi-restraints excluded: chain F residue 1372 THR Chi-restraints excluded: chain F residue 1373 ASP Chi-restraints excluded: chain F residue 1407 ILE Chi-restraints excluded: chain F residue 1417 LEU Chi-restraints excluded: chain F residue 1439 GLU Chi-restraints excluded: chain F residue 1472 GLU Chi-restraints excluded: chain F residue 1503 THR Chi-restraints excluded: chain F residue 1528 VAL Chi-restraints excluded: chain F residue 1624 GLN Chi-restraints excluded: chain F residue 1629 LEU Chi-restraints excluded: chain F residue 1636 LEU Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 380 TYR Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain I residue 647 GLN Chi-restraints excluded: chain I residue 678 GLN Chi-restraints excluded: chain I residue 690 GLN Chi-restraints excluded: chain I residue 745 TYR Chi-restraints excluded: chain I residue 771 ASN Chi-restraints excluded: chain I residue 821 ILE Chi-restraints excluded: chain I residue 823 LYS Chi-restraints excluded: chain J residue 368 ASP Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 411 ASN Chi-restraints excluded: chain J residue 444 ILE Chi-restraints excluded: chain J residue 461 HIS Chi-restraints excluded: chain K residue 299 TRP Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 404 ARG Chi-restraints excluded: chain K residue 448 GLU Chi-restraints excluded: chain L residue 695 GLN Chi-restraints excluded: chain L residue 745 TYR Chi-restraints excluded: chain L residue 750 THR Chi-restraints excluded: chain L residue 771 ASN Chi-restraints excluded: chain L residue 793 LEU Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 80 PHE Chi-restraints excluded: chain Z residue 84 ASP Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 116 LYS Chi-restraints excluded: chain Z residue 119 GLU Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 122 LEU Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 129 LEU Chi-restraints excluded: chain Z residue 139 PHE Chi-restraints excluded: chain Z residue 388 THR Chi-restraints excluded: chain Z residue 394 TYR Chi-restraints excluded: chain Z residue 409 LEU Chi-restraints excluded: chain Z residue 440 LEU Chi-restraints excluded: chain Z residue 451 ASP Chi-restraints excluded: chain Z residue 589 LEU Chi-restraints excluded: chain Z residue 630 ARG Chi-restraints excluded: chain Z residue 637 ILE Chi-restraints excluded: chain Z residue 716 LEU Chi-restraints excluded: chain Z residue 776 ILE Chi-restraints excluded: chain Z residue 804 ASP Chi-restraints excluded: chain Z residue 808 ASN Chi-restraints excluded: chain Z residue 824 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 279 optimal weight: 9.9990 chunk 747 optimal weight: 20.0000 chunk 164 optimal weight: 20.0000 chunk 487 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 chunk 831 optimal weight: 10.0000 chunk 689 optimal weight: 2.9990 chunk 384 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 274 optimal weight: 40.0000 chunk 436 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN C 383 HIS ** D 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1318 HIS ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 571 ASN E 788 HIS E 804 GLN E 865 ASN E 983 ASN E1001 ASN ** E1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1237 ASN E1413 ASN E1492 HIS E1613 ASN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 GLN ** F 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 557 ASN ** F 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 686 ASN ** F 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 772 ASN ** F1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1299 ASN G 282 GLN ** G 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 698 GLN ** I 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 328 GLN ** J 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 418 GLN ** L 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 60 ASN Z 141 ASN Z 227 GLN ** Z 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 464 ASN Z 563 ASN Z 738 GLN ** Z 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4783 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 68075 Z= 0.421 Angle : 0.897 16.339 92300 Z= 0.463 Chirality : 0.050 0.316 10884 Planarity : 0.006 0.159 11817 Dihedral : 7.034 86.084 9231 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.76 % Favored : 89.86 % Rotamer: Outliers : 4.51 % Allowed : 17.98 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.05 % Twisted Proline : 1.29 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.09), residues: 8584 helix: 0.12 (0.07), residues: 5065 sheet: 0.23 (0.27), residues: 379 loop : -2.62 (0.11), residues: 3140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 212 HIS 0.014 0.002 HIS E1429 PHE 0.046 0.003 PHE F 791 TYR 0.051 0.002 TYR G 387 ARG 0.018 0.001 ARG E 862 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 7900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 524 time to evaluate : 5.807 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 501 MET cc_start: 0.3325 (ppp) cc_final: 0.3117 (ppp) REVERT: A 739 MET cc_start: 0.3051 (ptt) cc_final: 0.2478 (mtm) REVERT: A 819 MET cc_start: -0.1045 (mtp) cc_final: -0.3887 (mmm) REVERT: C 388 MET cc_start: -0.0262 (mmm) cc_final: -0.1900 (ptm) REVERT: C 487 LYS cc_start: 0.2110 (tptm) cc_final: 0.1606 (ttpt) REVERT: C 861 GLN cc_start: 0.5406 (tt0) cc_final: 0.4886 (mm-40) REVERT: C 1104 LYS cc_start: 0.1859 (tttt) cc_final: 0.1540 (mmmt) REVERT: C 1289 MET cc_start: 0.2375 (tpp) cc_final: 0.2039 (tpp) REVERT: C 1387 HIS cc_start: 0.5223 (OUTLIER) cc_final: 0.4645 (t70) REVERT: D 199 ASN cc_start: 0.3625 (m-40) cc_final: 0.2840 (t0) REVERT: D 207 MET cc_start: 0.2194 (mmt) cc_final: 0.0878 (mmm) REVERT: D 327 MET cc_start: 0.0898 (mmm) cc_final: 0.0549 (ttt) REVERT: D 586 LEU cc_start: -0.0995 (OUTLIER) cc_final: -0.1354 (tt) REVERT: E 254 SER cc_start: 0.8086 (OUTLIER) cc_final: 0.7851 (t) REVERT: E 321 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7077 (tt) REVERT: E 457 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6607 (mp) REVERT: E 648 ARG cc_start: 0.7067 (mtt90) cc_final: 0.6083 (ptp-170) REVERT: E 764 LYS cc_start: 0.6648 (OUTLIER) cc_final: 0.6338 (ttmm) REVERT: E 771 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5259 (mt) REVERT: E 781 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7353 (t0) REVERT: E 808 THR cc_start: 0.8617 (p) cc_final: 0.8363 (p) REVERT: E 854 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7482 (tp) REVERT: E 878 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7679 (m-10) REVERT: E 901 ILE cc_start: 0.7450 (pt) cc_final: 0.7200 (pt) REVERT: E 909 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7064 (pt0) REVERT: E 1210 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7652 (tt) REVERT: F 207 MET cc_start: 0.1431 (tmm) cc_final: -0.0611 (mtt) REVERT: F 533 LEU cc_start: -0.0186 (OUTLIER) cc_final: -0.0728 (mt) REVERT: F 577 HIS cc_start: 0.3316 (OUTLIER) cc_final: 0.2441 (t70) REVERT: F 729 MET cc_start: 0.5322 (OUTLIER) cc_final: 0.4605 (pmm) REVERT: F 739 ARG cc_start: 0.2429 (OUTLIER) cc_final: 0.0448 (mmt180) REVERT: F 1056 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7846 (pt) REVERT: F 1138 PHE cc_start: 0.6450 (OUTLIER) cc_final: 0.6223 (t80) REVERT: F 1142 GLU cc_start: 0.3375 (OUTLIER) cc_final: 0.1676 (mt-10) REVERT: F 1195 PHE cc_start: 0.4771 (OUTLIER) cc_final: 0.3179 (m-10) REVERT: F 1373 ASP cc_start: 0.7050 (OUTLIER) cc_final: 0.5931 (t70) REVERT: F 1382 TYR cc_start: 0.4930 (t80) cc_final: 0.4535 (t80) REVERT: G 319 GLU cc_start: 0.7181 (tp30) cc_final: 0.5113 (pt0) REVERT: I 654 HIS cc_start: 0.2535 (t-170) cc_final: 0.2271 (t70) REVERT: I 678 GLN cc_start: 0.5105 (OUTLIER) cc_final: 0.3804 (tp-100) REVERT: J 444 ILE cc_start: 0.5936 (OUTLIER) cc_final: 0.5429 (tp) REVERT: J 463 LYS cc_start: 0.7220 (mmpt) cc_final: 0.6946 (mtmm) REVERT: K 404 ARG cc_start: 0.3186 (OUTLIER) cc_final: 0.2084 (ttm-80) REVERT: K 440 PHE cc_start: 0.1989 (OUTLIER) cc_final: 0.1783 (m-80) REVERT: K 469 ARG cc_start: 0.5352 (OUTLIER) cc_final: 0.5096 (mmp80) REVERT: K 518 ARG cc_start: 0.6677 (tmm-80) cc_final: 0.6145 (mmp-170) REVERT: L 771 ASN cc_start: 0.7305 (OUTLIER) cc_final: 0.6633 (p0) REVERT: L 799 SER cc_start: 0.7576 (OUTLIER) cc_final: 0.7345 (p) REVERT: L 823 LYS cc_start: 0.2945 (mtmm) cc_final: 0.2496 (pttp) REVERT: Z 80 PHE cc_start: 0.4737 (OUTLIER) cc_final: 0.4319 (m-80) REVERT: Z 122 LEU cc_start: 0.4284 (OUTLIER) cc_final: 0.3747 (tp) REVERT: Z 294 MET cc_start: 0.1743 (tmm) cc_final: 0.1445 (tpt) REVERT: Z 399 LYS cc_start: 0.3728 (mptt) cc_final: 0.3462 (mmtp) REVERT: Z 459 LEU cc_start: 0.6245 (tp) cc_final: 0.5545 (tt) REVERT: Z 661 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8148 (mt) outliers start: 326 outliers final: 201 residues processed: 795 average time/residue: 0.6169 time to fit residues: 869.7926 Evaluate side-chains 705 residues out of total 7900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 473 time to evaluate : 5.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 900 ASP Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 1013 LYS Chi-restraints excluded: chain C residue 1387 HIS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 783 ASP Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 980 SER Chi-restraints excluded: chain D residue 1053 MET Chi-restraints excluded: chain D residue 1081 CYS Chi-restraints excluded: chain D residue 1161 MET Chi-restraints excluded: chain D residue 1304 THR Chi-restraints excluded: chain D residue 1329 ASP Chi-restraints excluded: chain D residue 1407 ILE Chi-restraints excluded: chain D residue 1408 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 303 GLU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain E residue 435 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 600 ASN Chi-restraints excluded: chain E residue 601 VAL Chi-restraints excluded: chain E residue 602 VAL Chi-restraints excluded: chain E residue 644 ILE Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 694 ILE Chi-restraints excluded: chain E residue 699 GLU Chi-restraints excluded: chain E residue 736 ILE Chi-restraints excluded: chain E residue 749 ILE Chi-restraints excluded: chain E residue 753 TYR Chi-restraints excluded: chain E residue 764 LYS Chi-restraints excluded: chain E residue 771 LEU Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain E residue 781 ASP Chi-restraints excluded: chain E residue 795 ILE Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 826 SER Chi-restraints excluded: chain E residue 848 MET Chi-restraints excluded: chain E residue 854 LEU Chi-restraints excluded: chain E residue 878 PHE Chi-restraints excluded: chain E residue 889 THR Chi-restraints excluded: chain E residue 895 HIS Chi-restraints excluded: chain E residue 909 GLU Chi-restraints excluded: chain E residue 982 ILE Chi-restraints excluded: chain E residue 1008 THR Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1025 ASN Chi-restraints excluded: chain E residue 1028 THR Chi-restraints excluded: chain E residue 1047 LEU Chi-restraints excluded: chain E residue 1079 VAL Chi-restraints excluded: chain E residue 1154 GLU Chi-restraints excluded: chain E residue 1197 VAL Chi-restraints excluded: chain E residue 1201 ILE Chi-restraints excluded: chain E residue 1210 LEU Chi-restraints excluded: chain E residue 1211 ILE Chi-restraints excluded: chain E residue 1227 VAL Chi-restraints excluded: chain E residue 1238 ILE Chi-restraints excluded: chain E residue 1261 ILE Chi-restraints excluded: chain E residue 1262 LEU Chi-restraints excluded: chain E residue 1297 LYS Chi-restraints excluded: chain E residue 1316 LEU Chi-restraints excluded: chain E residue 1340 PHE Chi-restraints excluded: chain E residue 1453 ILE Chi-restraints excluded: chain E residue 1463 SER Chi-restraints excluded: chain E residue 1466 TYR Chi-restraints excluded: chain E residue 1469 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 163 ASN Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 416 TYR Chi-restraints excluded: chain F residue 533 LEU Chi-restraints excluded: chain F residue 577 HIS Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 656 VAL Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 713 PHE Chi-restraints excluded: chain F residue 716 LEU Chi-restraints excluded: chain F residue 717 ILE Chi-restraints excluded: chain F residue 719 ILE Chi-restraints excluded: chain F residue 729 MET Chi-restraints excluded: chain F residue 739 ARG Chi-restraints excluded: chain F residue 780 ILE Chi-restraints excluded: chain F residue 781 LEU Chi-restraints excluded: chain F residue 786 THR Chi-restraints excluded: chain F residue 837 TYR Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 926 LEU Chi-restraints excluded: chain F residue 928 LEU Chi-restraints excluded: chain F residue 936 ILE Chi-restraints excluded: chain F residue 965 LEU Chi-restraints excluded: chain F residue 986 LEU Chi-restraints excluded: chain F residue 995 VAL Chi-restraints excluded: chain F residue 1041 PHE Chi-restraints excluded: chain F residue 1056 LEU Chi-restraints excluded: chain F residue 1075 LEU Chi-restraints excluded: chain F residue 1086 LEU Chi-restraints excluded: chain F residue 1128 ASP Chi-restraints excluded: chain F residue 1138 PHE Chi-restraints excluded: chain F residue 1139 ILE Chi-restraints excluded: chain F residue 1142 GLU Chi-restraints excluded: chain F residue 1144 VAL Chi-restraints excluded: chain F residue 1181 VAL Chi-restraints excluded: chain F residue 1191 SER Chi-restraints excluded: chain F residue 1195 PHE Chi-restraints excluded: chain F residue 1280 ILE Chi-restraints excluded: chain F residue 1299 ASN Chi-restraints excluded: chain F residue 1313 ILE Chi-restraints excluded: chain F residue 1315 THR Chi-restraints excluded: chain F residue 1347 ILE Chi-restraints excluded: chain F residue 1348 THR Chi-restraints excluded: chain F residue 1373 ASP Chi-restraints excluded: chain F residue 1417 LEU Chi-restraints excluded: chain F residue 1421 VAL Chi-restraints excluded: chain F residue 1439 GLU Chi-restraints excluded: chain F residue 1451 THR Chi-restraints excluded: chain F residue 1479 LEU Chi-restraints excluded: chain F residue 1486 LEU Chi-restraints excluded: chain F residue 1503 THR Chi-restraints excluded: chain F residue 1624 GLN Chi-restraints excluded: chain F residue 1629 LEU Chi-restraints excluded: chain F residue 1636 LEU Chi-restraints excluded: chain G residue 282 GLN Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 372 PHE Chi-restraints excluded: chain G residue 380 TYR Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 450 PHE Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain I residue 659 THR Chi-restraints excluded: chain I residue 678 GLN Chi-restraints excluded: chain I residue 690 GLN Chi-restraints excluded: chain I residue 712 ASP Chi-restraints excluded: chain I residue 728 THR Chi-restraints excluded: chain I residue 764 SER Chi-restraints excluded: chain I residue 821 ILE Chi-restraints excluded: chain I residue 823 LYS Chi-restraints excluded: chain J residue 368 ASP Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 411 ASN Chi-restraints excluded: chain J residue 434 THR Chi-restraints excluded: chain J residue 444 ILE Chi-restraints excluded: chain K residue 299 TRP Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 404 ARG Chi-restraints excluded: chain K residue 440 PHE Chi-restraints excluded: chain K residue 448 GLU Chi-restraints excluded: chain K residue 469 ARG Chi-restraints excluded: chain L residue 745 TYR Chi-restraints excluded: chain L residue 750 THR Chi-restraints excluded: chain L residue 757 SER Chi-restraints excluded: chain L residue 771 ASN Chi-restraints excluded: chain L residue 793 LEU Chi-restraints excluded: chain L residue 799 SER Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 80 PHE Chi-restraints excluded: chain Z residue 84 ASP Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 116 LYS Chi-restraints excluded: chain Z residue 119 GLU Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 122 LEU Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 139 PHE Chi-restraints excluded: chain Z residue 140 ILE Chi-restraints excluded: chain Z residue 234 ILE Chi-restraints excluded: chain Z residue 388 THR Chi-restraints excluded: chain Z residue 394 TYR Chi-restraints excluded: chain Z residue 409 LEU Chi-restraints excluded: chain Z residue 514 LYS Chi-restraints excluded: chain Z residue 519 ASP Chi-restraints excluded: chain Z residue 588 VAL Chi-restraints excluded: chain Z residue 589 LEU Chi-restraints excluded: chain Z residue 630 ARG Chi-restraints excluded: chain Z residue 637 ILE Chi-restraints excluded: chain Z residue 661 LEU Chi-restraints excluded: chain Z residue 675 VAL Chi-restraints excluded: chain Z residue 686 VAL Chi-restraints excluded: chain Z residue 692 MET Chi-restraints excluded: chain Z residue 716 LEU Chi-restraints excluded: chain Z residue 776 ILE Chi-restraints excluded: chain Z residue 804 ASP Chi-restraints excluded: chain Z residue 808 ASN Chi-restraints excluded: chain Z residue 824 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 801 optimal weight: 2.9990 chunk 93 optimal weight: 50.0000 chunk 473 optimal weight: 0.2980 chunk 606 optimal weight: 2.9990 chunk 470 optimal weight: 0.8980 chunk 699 optimal weight: 0.8980 chunk 464 optimal weight: 3.9990 chunk 827 optimal weight: 5.9990 chunk 518 optimal weight: 4.9990 chunk 504 optimal weight: 9.9990 chunk 382 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1253 GLN E 193 GLN ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 215 GLN E 219 GLN ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 804 GLN E 983 ASN E1114 GLN E1413 ASN E1492 HIS ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 GLN F 219 HIS F 334 GLN ** F 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN ** F 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1027 GLN ** G 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 378 HIS H 402 GLN ** I 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 663 ASN I 749 GLN ** J 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 654 HIS ** L 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 703 GLN ** L 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 227 GLN ** Z 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 301 ASN Z 464 ASN Z 563 ASN ** Z 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4599 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 68075 Z= 0.208 Angle : 0.741 17.108 92300 Z= 0.378 Chirality : 0.044 0.305 10884 Planarity : 0.005 0.155 11817 Dihedral : 6.461 87.249 9225 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.22 % Favored : 91.46 % Rotamer: Outliers : 3.47 % Allowed : 19.42 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.05 % Twisted Proline : 0.86 % Twisted General : 0.04 % 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: -0.88 (0.09), residues: 8584 helix: 0.49 (0.07), residues: 5081 sheet: 0.30 (0.27), residues: 379 loop : -2.55 (0.11), residues: 3124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E1495 HIS 0.010 0.001 HIS E1429 PHE 0.067 0.002 PHE F 572 TYR 0.053 0.002 TYR G 387 ARG 0.011 0.000 ARG F1247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 7900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 531 time to evaluate : 5.740 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: A 739 MET cc_start: 0.2961 (ptt) cc_final: 0.2559 (mtm) REVERT: A 819 MET cc_start: -0.0718 (mtp) cc_final: -0.3791 (mmm) REVERT: C 388 MET cc_start: -0.0817 (mmm) cc_final: -0.2252 (ptm) REVERT: C 861 GLN cc_start: 0.5365 (tt0) cc_final: 0.4856 (mm-40) REVERT: C 1048 MET cc_start: 0.0353 (mmp) cc_final: -0.0412 (mmm) REVERT: C 1104 LYS cc_start: 0.1599 (tttt) cc_final: 0.1330 (mmmt) REVERT: C 1379 VAL cc_start: 0.0757 (OUTLIER) cc_final: 0.0550 (t) REVERT: C 1387 HIS cc_start: 0.5189 (OUTLIER) cc_final: 0.4637 (t70) REVERT: D 199 ASN cc_start: 0.3604 (m-40) cc_final: 0.2817 (t0) REVERT: D 207 MET cc_start: 0.1929 (mmt) cc_final: 0.0557 (mmm) REVERT: D 327 MET cc_start: 0.0896 (mmm) cc_final: 0.0550 (ttt) REVERT: D 586 LEU cc_start: -0.1023 (OUTLIER) cc_final: -0.1383 (tt) REVERT: D 860 ILE cc_start: -0.1598 (OUTLIER) cc_final: -0.1816 (mm) REVERT: E 321 ILE cc_start: 0.7343 (OUTLIER) cc_final: 0.6823 (tt) REVERT: E 445 LEU cc_start: 0.8775 (mt) cc_final: 0.8527 (mp) REVERT: E 457 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6441 (mp) REVERT: E 648 ARG cc_start: 0.7060 (mtt90) cc_final: 0.5854 (ptp-170) REVERT: E 721 GLU cc_start: 0.6388 (mm-30) cc_final: 0.6132 (mm-30) REVERT: E 764 LYS cc_start: 0.6311 (OUTLIER) cc_final: 0.5932 (ttmm) REVERT: E 771 LEU cc_start: 0.6191 (OUTLIER) cc_final: 0.5556 (mt) REVERT: E 781 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7211 (t0) REVERT: E 878 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7390 (m-10) REVERT: F 207 MET cc_start: 0.1240 (tmm) cc_final: -0.0570 (mtt) REVERT: F 533 LEU cc_start: 0.0904 (OUTLIER) cc_final: 0.0419 (mt) REVERT: F 845 ASP cc_start: 0.7629 (t0) cc_final: 0.7153 (t70) REVERT: F 1027 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7462 (tm-30) REVERT: F 1138 PHE cc_start: 0.6085 (OUTLIER) cc_final: 0.5568 (t80) REVERT: F 1142 GLU cc_start: 0.3240 (OUTLIER) cc_final: 0.2143 (mm-30) REVERT: F 1195 PHE cc_start: 0.5299 (OUTLIER) cc_final: 0.3800 (m-10) REVERT: F 1196 SER cc_start: 0.6568 (t) cc_final: 0.6293 (m) REVERT: F 1373 ASP cc_start: 0.6393 (OUTLIER) cc_final: 0.4915 (t70) REVERT: H 339 MET cc_start: 0.2650 (mmm) cc_final: 0.1434 (mmm) REVERT: I 661 LYS cc_start: 0.7207 (mmmt) cc_final: 0.6755 (mtmt) REVERT: I 678 GLN cc_start: 0.4891 (OUTLIER) cc_final: 0.3874 (tp-100) REVERT: J 303 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.7025 (pm20) REVERT: J 444 ILE cc_start: 0.5832 (OUTLIER) cc_final: 0.5317 (tp) REVERT: J 463 LYS cc_start: 0.7449 (mmpt) cc_final: 0.7242 (mtmm) REVERT: K 518 ARG cc_start: 0.6550 (tmm-80) cc_final: 0.6084 (mmp-170) REVERT: L 749 GLN cc_start: 0.4584 (mm-40) cc_final: 0.4155 (tp40) REVERT: L 771 ASN cc_start: 0.7470 (OUTLIER) cc_final: 0.6911 (p0) REVERT: L 799 SER cc_start: 0.7419 (OUTLIER) cc_final: 0.7036 (p) REVERT: L 823 LYS cc_start: 0.3482 (mtmm) cc_final: 0.2863 (pttm) REVERT: Z 80 PHE cc_start: 0.4875 (OUTLIER) cc_final: 0.4471 (m-80) REVERT: Z 122 LEU cc_start: 0.4071 (OUTLIER) cc_final: 0.2708 (pp) REVERT: Z 294 MET cc_start: 0.1754 (tmm) cc_final: 0.1509 (tpt) REVERT: Z 399 LYS cc_start: 0.3552 (mptt) cc_final: 0.3082 (mmtp) REVERT: Z 459 LEU cc_start: 0.6089 (tp) cc_final: 0.5488 (tt) REVERT: Z 661 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7999 (mt) outliers start: 251 outliers final: 177 residues processed: 737 average time/residue: 0.6236 time to fit residues: 810.9623 Evaluate side-chains 681 residues out of total 7900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 480 time to evaluate : 5.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 900 ASP Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 1013 LYS Chi-restraints excluded: chain C residue 1379 VAL Chi-restraints excluded: chain C residue 1387 HIS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 500 MET Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 783 ASP Chi-restraints excluded: chain D residue 810 ILE Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 860 ILE Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 980 SER Chi-restraints excluded: chain D residue 1053 MET Chi-restraints excluded: chain D residue 1161 MET Chi-restraints excluded: chain D residue 1183 LEU Chi-restraints excluded: chain D residue 1329 ASP Chi-restraints excluded: chain D residue 1384 ILE Chi-restraints excluded: chain D residue 1408 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 303 GLU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 435 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 602 VAL Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 676 LEU Chi-restraints excluded: chain E residue 699 GLU Chi-restraints excluded: chain E residue 753 TYR Chi-restraints excluded: chain E residue 764 LYS Chi-restraints excluded: chain E residue 771 LEU Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain E residue 781 ASP Chi-restraints excluded: chain E residue 795 ILE Chi-restraints excluded: chain E residue 804 GLN Chi-restraints excluded: chain E residue 826 SER Chi-restraints excluded: chain E residue 848 MET Chi-restraints excluded: chain E residue 878 PHE Chi-restraints excluded: chain E residue 889 THR Chi-restraints excluded: chain E residue 895 HIS Chi-restraints excluded: chain E residue 908 VAL Chi-restraints excluded: chain E residue 909 GLU Chi-restraints excluded: chain E residue 982 ILE Chi-restraints excluded: chain E residue 1012 VAL Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1028 THR Chi-restraints excluded: chain E residue 1079 VAL Chi-restraints excluded: chain E residue 1211 ILE Chi-restraints excluded: chain E residue 1227 VAL Chi-restraints excluded: chain E residue 1238 ILE Chi-restraints excluded: chain E residue 1262 LEU Chi-restraints excluded: chain E residue 1297 LYS Chi-restraints excluded: chain E residue 1316 LEU Chi-restraints excluded: chain E residue 1340 PHE Chi-restraints excluded: chain E residue 1453 ILE Chi-restraints excluded: chain E residue 1466 TYR Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 163 ASN Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 533 LEU Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 688 SER Chi-restraints excluded: chain F residue 713 PHE Chi-restraints excluded: chain F residue 717 ILE Chi-restraints excluded: chain F residue 719 ILE Chi-restraints excluded: chain F residue 786 THR Chi-restraints excluded: chain F residue 837 TYR Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 926 LEU Chi-restraints excluded: chain F residue 928 LEU Chi-restraints excluded: chain F residue 936 ILE Chi-restraints excluded: chain F residue 982 PHE Chi-restraints excluded: chain F residue 1027 GLN Chi-restraints excluded: chain F residue 1041 PHE Chi-restraints excluded: chain F residue 1056 LEU Chi-restraints excluded: chain F residue 1086 LEU Chi-restraints excluded: chain F residue 1128 ASP Chi-restraints excluded: chain F residue 1138 PHE Chi-restraints excluded: chain F residue 1139 ILE Chi-restraints excluded: chain F residue 1142 GLU Chi-restraints excluded: chain F residue 1144 VAL Chi-restraints excluded: chain F residue 1161 LEU Chi-restraints excluded: chain F residue 1181 VAL Chi-restraints excluded: chain F residue 1195 PHE Chi-restraints excluded: chain F residue 1219 VAL Chi-restraints excluded: chain F residue 1313 ILE Chi-restraints excluded: chain F residue 1315 THR Chi-restraints excluded: chain F residue 1347 ILE Chi-restraints excluded: chain F residue 1373 ASP Chi-restraints excluded: chain F residue 1407 ILE Chi-restraints excluded: chain F residue 1417 LEU Chi-restraints excluded: chain F residue 1439 GLU Chi-restraints excluded: chain F residue 1472 GLU Chi-restraints excluded: chain F residue 1486 LEU Chi-restraints excluded: chain F residue 1503 THR Chi-restraints excluded: chain F residue 1526 ILE Chi-restraints excluded: chain F residue 1528 VAL Chi-restraints excluded: chain F residue 1543 LEU Chi-restraints excluded: chain F residue 1624 GLN Chi-restraints excluded: chain F residue 1629 LEU Chi-restraints excluded: chain F residue 1636 LEU Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 333 ILE Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain G residue 380 TYR Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 450 PHE Chi-restraints excluded: chain H residue 378 HIS Chi-restraints excluded: chain H residue 402 GLN Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain I residue 678 GLN Chi-restraints excluded: chain I residue 690 GLN Chi-restraints excluded: chain I residue 712 ASP Chi-restraints excluded: chain I residue 728 THR Chi-restraints excluded: chain I residue 764 SER Chi-restraints excluded: chain I residue 771 ASN Chi-restraints excluded: chain I residue 821 ILE Chi-restraints excluded: chain I residue 823 LYS Chi-restraints excluded: chain J residue 303 GLU Chi-restraints excluded: chain J residue 368 ASP Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 378 HIS Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 411 ASN Chi-restraints excluded: chain J residue 434 THR Chi-restraints excluded: chain J residue 444 ILE Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain K residue 448 GLU Chi-restraints excluded: chain L residue 745 TYR Chi-restraints excluded: chain L residue 750 THR Chi-restraints excluded: chain L residue 771 ASN Chi-restraints excluded: chain L residue 793 LEU Chi-restraints excluded: chain L residue 799 SER Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 80 PHE Chi-restraints excluded: chain Z residue 84 ASP Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 116 LYS Chi-restraints excluded: chain Z residue 119 GLU Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 122 LEU Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 139 PHE Chi-restraints excluded: chain Z residue 140 ILE Chi-restraints excluded: chain Z residue 234 ILE Chi-restraints excluded: chain Z residue 394 TYR Chi-restraints excluded: chain Z residue 409 LEU Chi-restraints excluded: chain Z residue 514 LYS Chi-restraints excluded: chain Z residue 589 LEU Chi-restraints excluded: chain Z residue 630 ARG Chi-restraints excluded: chain Z residue 637 ILE Chi-restraints excluded: chain Z residue 652 ILE Chi-restraints excluded: chain Z residue 661 LEU Chi-restraints excluded: chain Z residue 675 VAL Chi-restraints excluded: chain Z residue 686 VAL Chi-restraints excluded: chain Z residue 708 VAL Chi-restraints excluded: chain Z residue 776 ILE Chi-restraints excluded: chain Z residue 804 ASP Chi-restraints excluded: chain Z residue 808 ASN Chi-restraints excluded: chain Z residue 824 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 512 optimal weight: 40.0000 chunk 330 optimal weight: 3.9990 chunk 494 optimal weight: 7.9990 chunk 249 optimal weight: 6.9990 chunk 162 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 chunk 526 optimal weight: 2.9990 chunk 564 optimal weight: 6.9990 chunk 409 optimal weight: 1.9990 chunk 77 optimal weight: 40.0000 chunk 650 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 486 GLN ** D 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1158 HIS ** D1253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 GLN ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1306 ASN E1492 HIS ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 GLN F 334 GLN ** F 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1222 ASN G 282 GLN ** G 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 362 ASN ** H 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 654 HIS I 657 GLN I 756 ASN J 324 GLN ** J 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 418 GLN L 654 HIS ** L 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 227 GLN ** Z 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4769 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 68075 Z= 0.338 Angle : 0.833 19.414 92300 Z= 0.426 Chirality : 0.047 0.293 10884 Planarity : 0.005 0.158 11817 Dihedral : 6.612 96.140 9218 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.35 % Allowed : 9.52 % Favored : 90.13 % Rotamer: Outliers : 3.75 % Allowed : 19.89 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.05 % Twisted Proline : 1.29 % 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: -1.05 (0.09), residues: 8584 helix: 0.29 (0.07), residues: 5099 sheet: 0.23 (0.27), residues: 374 loop : -2.50 (0.11), residues: 3111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP H 335 HIS 0.044 0.002 HIS H 378 PHE 0.038 0.002 PHE F 791 TYR 0.060 0.002 TYR F1156 ARG 0.013 0.001 ARG K 469 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 7900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 516 time to evaluate : 5.713 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: A 53 VAL cc_start: 0.2929 (OUTLIER) cc_final: 0.2159 (p) REVERT: A 57 ARG cc_start: 0.5356 (mtm-85) cc_final: 0.4497 (mtm180) REVERT: A 501 MET cc_start: 0.2314 (ppp) cc_final: 0.2003 (ppp) REVERT: A 739 MET cc_start: 0.3042 (ptt) cc_final: 0.2755 (mtm) REVERT: A 819 MET cc_start: -0.0649 (mtp) cc_final: -0.3821 (mmm) REVERT: C 388 MET cc_start: -0.0744 (mmm) cc_final: -0.2193 (ptm) REVERT: C 861 GLN cc_start: 0.5410 (tt0) cc_final: 0.4873 (mm-40) REVERT: C 1048 MET cc_start: 0.0542 (mmp) cc_final: -0.0244 (mmm) REVERT: C 1104 LYS cc_start: 0.1876 (tttt) cc_final: 0.1520 (mmmt) REVERT: C 1387 HIS cc_start: 0.5272 (OUTLIER) cc_final: 0.4495 (t70) REVERT: D 199 ASN cc_start: 0.3935 (m-40) cc_final: 0.3179 (t0) REVERT: D 207 MET cc_start: 0.2143 (mmt) cc_final: 0.0635 (mmm) REVERT: D 327 MET cc_start: 0.0917 (mmm) cc_final: 0.0573 (ttt) REVERT: D 586 LEU cc_start: -0.1004 (OUTLIER) cc_final: -0.1344 (tt) REVERT: E 254 SER cc_start: 0.8058 (OUTLIER) cc_final: 0.7847 (t) REVERT: E 318 HIS cc_start: 0.5896 (t70) cc_final: 0.5651 (t-90) REVERT: E 321 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.6998 (tt) REVERT: E 457 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6591 (mp) REVERT: E 648 ARG cc_start: 0.7119 (mtt90) cc_final: 0.6125 (ptp-170) REVERT: E 764 LYS cc_start: 0.6564 (OUTLIER) cc_final: 0.6252 (ttmm) REVERT: E 771 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.5621 (mt) REVERT: E 781 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7447 (t0) REVERT: E 804 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.5541 (pp30) REVERT: E 854 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7452 (tp) REVERT: E 878 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7675 (m-10) REVERT: E 1650 SER cc_start: 0.6277 (m) cc_final: 0.6008 (p) REVERT: F 207 MET cc_start: 0.1896 (tmm) cc_final: -0.0212 (mtt) REVERT: F 398 MET cc_start: 0.3011 (mtt) cc_final: 0.2552 (ptp) REVERT: F 533 LEU cc_start: 0.0186 (OUTLIER) cc_final: -0.0522 (mt) REVERT: F 739 ARG cc_start: 0.2588 (OUTLIER) cc_final: 0.0464 (mmt180) REVERT: F 1027 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: F 1142 GLU cc_start: 0.3399 (OUTLIER) cc_final: 0.1909 (mm-30) REVERT: F 1195 PHE cc_start: 0.4933 (OUTLIER) cc_final: 0.3516 (m-10) REVERT: F 1309 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.6267 (mt) REVERT: F 1373 ASP cc_start: 0.6602 (OUTLIER) cc_final: 0.6150 (t70) REVERT: F 1382 TYR cc_start: 0.4599 (t80) cc_final: 0.3993 (t80) REVERT: H 339 MET cc_start: 0.2066 (mmm) cc_final: 0.1792 (mmp) REVERT: H 445 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8869 (tm-30) REVERT: I 678 GLN cc_start: 0.4889 (OUTLIER) cc_final: 0.3906 (tp-100) REVERT: J 303 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7163 (pm20) REVERT: J 444 ILE cc_start: 0.5966 (OUTLIER) cc_final: 0.5443 (tp) REVERT: K 414 LYS cc_start: 0.3549 (tttt) cc_final: 0.3210 (tptp) REVERT: K 440 PHE cc_start: 0.2108 (OUTLIER) cc_final: 0.1777 (m-80) REVERT: L 799 SER cc_start: 0.7502 (OUTLIER) cc_final: 0.7096 (p) REVERT: L 823 LYS cc_start: 0.3924 (mtmm) cc_final: 0.3535 (pttm) REVERT: Z 80 PHE cc_start: 0.4789 (OUTLIER) cc_final: 0.4450 (m-80) REVERT: Z 122 LEU cc_start: 0.4292 (OUTLIER) cc_final: 0.3841 (tp) REVERT: Z 234 ILE cc_start: 0.5742 (OUTLIER) cc_final: 0.5478 (mp) REVERT: Z 294 MET cc_start: 0.2039 (tmm) cc_final: 0.1731 (tpt) REVERT: Z 399 LYS cc_start: 0.3663 (mptt) cc_final: 0.3354 (mmtp) REVERT: Z 459 LEU cc_start: 0.6245 (tp) cc_final: 0.5513 (tt) outliers start: 271 outliers final: 207 residues processed: 734 average time/residue: 0.6093 time to fit residues: 786.4774 Evaluate side-chains 713 residues out of total 7900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 479 time to evaluate : 5.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 900 ASP Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 1013 LYS Chi-restraints excluded: chain C residue 1387 HIS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 260 HIS Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 783 ASP Chi-restraints excluded: chain D residue 810 ILE Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 886 ASN Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 980 SER Chi-restraints excluded: chain D residue 1053 MET Chi-restraints excluded: chain D residue 1161 MET Chi-restraints excluded: chain D residue 1212 GLU Chi-restraints excluded: chain D residue 1304 THR Chi-restraints excluded: chain D residue 1329 ASP Chi-restraints excluded: chain D residue 1384 ILE Chi-restraints excluded: chain D residue 1407 ILE Chi-restraints excluded: chain D residue 1408 VAL Chi-restraints excluded: chain D residue 1421 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 303 GLU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 323 TYR Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain E residue 435 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 600 ASN Chi-restraints excluded: chain E residue 602 VAL Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 694 ILE Chi-restraints excluded: chain E residue 699 GLU Chi-restraints excluded: chain E residue 753 TYR Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain E residue 764 LYS Chi-restraints excluded: chain E residue 771 LEU Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain E residue 781 ASP Chi-restraints excluded: chain E residue 795 ILE Chi-restraints excluded: chain E residue 804 GLN Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 826 SER Chi-restraints excluded: chain E residue 830 THR Chi-restraints excluded: chain E residue 848 MET Chi-restraints excluded: chain E residue 854 LEU Chi-restraints excluded: chain E residue 878 PHE Chi-restraints excluded: chain E residue 889 THR Chi-restraints excluded: chain E residue 895 HIS Chi-restraints excluded: chain E residue 909 GLU Chi-restraints excluded: chain E residue 982 ILE Chi-restraints excluded: chain E residue 1012 VAL Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1025 ASN Chi-restraints excluded: chain E residue 1028 THR Chi-restraints excluded: chain E residue 1079 VAL Chi-restraints excluded: chain E residue 1197 VAL Chi-restraints excluded: chain E residue 1211 ILE Chi-restraints excluded: chain E residue 1215 VAL Chi-restraints excluded: chain E residue 1227 VAL Chi-restraints excluded: chain E residue 1238 ILE Chi-restraints excluded: chain E residue 1262 LEU Chi-restraints excluded: chain E residue 1297 LYS Chi-restraints excluded: chain E residue 1316 LEU Chi-restraints excluded: chain E residue 1340 PHE Chi-restraints excluded: chain E residue 1453 ILE Chi-restraints excluded: chain E residue 1465 LEU Chi-restraints excluded: chain E residue 1466 TYR Chi-restraints excluded: chain E residue 1469 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 163 ASN Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 416 TYR Chi-restraints excluded: chain F residue 533 LEU Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 609 LEU Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 713 PHE Chi-restraints excluded: chain F residue 717 ILE Chi-restraints excluded: chain F residue 719 ILE Chi-restraints excluded: chain F residue 730 VAL Chi-restraints excluded: chain F residue 739 ARG Chi-restraints excluded: chain F residue 781 LEU Chi-restraints excluded: chain F residue 786 THR Chi-restraints excluded: chain F residue 837 TYR Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 926 LEU Chi-restraints excluded: chain F residue 928 LEU Chi-restraints excluded: chain F residue 936 ILE Chi-restraints excluded: chain F residue 982 PHE Chi-restraints excluded: chain F residue 995 VAL Chi-restraints excluded: chain F residue 996 LEU Chi-restraints excluded: chain F residue 1027 GLN Chi-restraints excluded: chain F residue 1041 PHE Chi-restraints excluded: chain F residue 1056 LEU Chi-restraints excluded: chain F residue 1128 ASP Chi-restraints excluded: chain F residue 1139 ILE Chi-restraints excluded: chain F residue 1142 GLU Chi-restraints excluded: chain F residue 1144 VAL Chi-restraints excluded: chain F residue 1178 LEU Chi-restraints excluded: chain F residue 1181 VAL Chi-restraints excluded: chain F residue 1195 PHE Chi-restraints excluded: chain F residue 1208 GLU Chi-restraints excluded: chain F residue 1239 PHE Chi-restraints excluded: chain F residue 1309 LEU Chi-restraints excluded: chain F residue 1313 ILE Chi-restraints excluded: chain F residue 1315 THR Chi-restraints excluded: chain F residue 1347 ILE Chi-restraints excluded: chain F residue 1373 ASP Chi-restraints excluded: chain F residue 1407 ILE Chi-restraints excluded: chain F residue 1417 LEU Chi-restraints excluded: chain F residue 1439 GLU Chi-restraints excluded: chain F residue 1451 THR Chi-restraints excluded: chain F residue 1486 LEU Chi-restraints excluded: chain F residue 1503 THR Chi-restraints excluded: chain F residue 1543 LEU Chi-restraints excluded: chain F residue 1624 GLN Chi-restraints excluded: chain F residue 1629 LEU Chi-restraints excluded: chain F residue 1636 LEU Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 303 GLU Chi-restraints excluded: chain G residue 308 ILE Chi-restraints excluded: chain G residue 340 ILE Chi-restraints excluded: chain G residue 380 TYR Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 450 PHE Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain H residue 402 GLN Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain I residue 659 THR Chi-restraints excluded: chain I residue 678 GLN Chi-restraints excluded: chain I residue 712 ASP Chi-restraints excluded: chain I residue 728 THR Chi-restraints excluded: chain I residue 764 SER Chi-restraints excluded: chain I residue 771 ASN Chi-restraints excluded: chain I residue 821 ILE Chi-restraints excluded: chain I residue 823 LYS Chi-restraints excluded: chain J residue 303 GLU Chi-restraints excluded: chain J residue 368 ASP Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 378 HIS Chi-restraints excluded: chain J residue 384 LEU Chi-restraints excluded: chain J residue 411 ASN Chi-restraints excluded: chain J residue 415 THR Chi-restraints excluded: chain J residue 434 THR Chi-restraints excluded: chain J residue 444 ILE Chi-restraints excluded: chain K residue 299 TRP Chi-restraints excluded: chain K residue 353 TYR Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain K residue 440 PHE Chi-restraints excluded: chain K residue 448 GLU Chi-restraints excluded: chain L residue 745 TYR Chi-restraints excluded: chain L residue 750 THR Chi-restraints excluded: chain L residue 771 ASN Chi-restraints excluded: chain L residue 793 LEU Chi-restraints excluded: chain L residue 799 SER Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 80 PHE Chi-restraints excluded: chain Z residue 84 ASP Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 116 LYS Chi-restraints excluded: chain Z residue 119 GLU Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 122 LEU Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 139 PHE Chi-restraints excluded: chain Z residue 140 ILE Chi-restraints excluded: chain Z residue 234 ILE Chi-restraints excluded: chain Z residue 388 THR Chi-restraints excluded: chain Z residue 394 TYR Chi-restraints excluded: chain Z residue 409 LEU Chi-restraints excluded: chain Z residue 440 LEU Chi-restraints excluded: chain Z residue 514 LYS Chi-restraints excluded: chain Z residue 554 VAL Chi-restraints excluded: chain Z residue 567 THR Chi-restraints excluded: chain Z residue 588 VAL Chi-restraints excluded: chain Z residue 589 LEU Chi-restraints excluded: chain Z residue 630 ARG Chi-restraints excluded: chain Z residue 637 ILE Chi-restraints excluded: chain Z residue 652 ILE Chi-restraints excluded: chain Z residue 675 VAL Chi-restraints excluded: chain Z residue 686 VAL Chi-restraints excluded: chain Z residue 708 VAL Chi-restraints excluded: chain Z residue 776 ILE Chi-restraints excluded: chain Z residue 804 ASP Chi-restraints excluded: chain Z residue 808 ASN Chi-restraints excluded: chain Z residue 824 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 753 optimal weight: 0.1980 chunk 793 optimal weight: 0.6980 chunk 723 optimal weight: 6.9990 chunk 771 optimal weight: 0.7980 chunk 792 optimal weight: 0.9990 chunk 464 optimal weight: 9.9990 chunk 336 optimal weight: 7.9990 chunk 605 optimal weight: 0.4980 chunk 236 optimal weight: 2.9990 chunk 697 optimal weight: 5.9990 chunk 729 optimal weight: 7.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 804 GLN E 865 ASN E 895 HIS ** E 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1492 HIS ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 ASN F 161 GLN ** F 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 378 HIS H 387 GLN H 402 GLN H 441 GLN ** J 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 654 HIS ** L 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 703 GLN L 774 ASN Z 227 GLN Z 464 ASN ** Z 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4573 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 68075 Z= 0.191 Angle : 0.746 16.645 92300 Z= 0.376 Chirality : 0.044 0.284 10884 Planarity : 0.004 0.153 11817 Dihedral : 6.180 94.202 9218 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.88 % Favored : 91.82 % Rotamer: Outliers : 2.86 % Allowed : 21.02 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.05 % Twisted Proline : 0.86 % Twisted General : 0.05 % 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: -0.70 (0.09), residues: 8584 helix: 0.64 (0.07), residues: 5094 sheet: 0.20 (0.27), residues: 378 loop : -2.45 (0.11), residues: 3112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP H 335 HIS 0.011 0.001 HIS H 378 PHE 0.072 0.001 PHE F 572 TYR 0.073 0.002 TYR F1156 ARG 0.007 0.000 ARG E 332 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 7900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 539 time to evaluate : 6.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 VAL cc_start: 0.2800 (OUTLIER) cc_final: 0.2000 (p) REVERT: A 57 ARG cc_start: 0.5330 (mtm-85) cc_final: 0.4586 (mtm180) REVERT: A 501 MET cc_start: 0.2360 (ppp) cc_final: 0.2021 (ppp) REVERT: A 739 MET cc_start: 0.3036 (ptt) cc_final: 0.2731 (mtm) REVERT: A 819 MET cc_start: 0.0116 (mtp) cc_final: -0.3232 (mmm) REVERT: C 388 MET cc_start: -0.0881 (mmm) cc_final: -0.2223 (ptm) REVERT: C 861 GLN cc_start: 0.5384 (tt0) cc_final: 0.4845 (mm-40) REVERT: C 1048 MET cc_start: -0.0110 (mmp) cc_final: -0.0809 (mmm) REVERT: C 1104 LYS cc_start: 0.1780 (tttt) cc_final: 0.1398 (mmmt) REVERT: C 1289 MET cc_start: 0.1029 (tpp) cc_final: 0.0574 (tpp) REVERT: C 1310 MET cc_start: -0.0390 (mmt) cc_final: -0.0863 (mpp) REVERT: C 1387 HIS cc_start: 0.5175 (OUTLIER) cc_final: 0.4487 (t70) REVERT: D 199 ASN cc_start: 0.4098 (m-40) cc_final: 0.3250 (t0) REVERT: D 207 MET cc_start: 0.2502 (mmt) cc_final: 0.0970 (mmm) REVERT: D 327 MET cc_start: 0.1114 (mmm) cc_final: 0.0738 (ttt) REVERT: D 586 LEU cc_start: -0.1008 (OUTLIER) cc_final: -0.1340 (tt) REVERT: D 1349 MET cc_start: 0.3485 (mmp) cc_final: 0.3026 (mmp) REVERT: E 254 SER cc_start: 0.8101 (OUTLIER) cc_final: 0.7895 (t) REVERT: E 321 ILE cc_start: 0.7365 (OUTLIER) cc_final: 0.7077 (tt) REVERT: E 457 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6491 (mp) REVERT: E 648 ARG cc_start: 0.7060 (mtt90) cc_final: 0.5793 (ptp-170) REVERT: E 764 LYS cc_start: 0.6272 (OUTLIER) cc_final: 0.5882 (tttp) REVERT: E 771 LEU cc_start: 0.5862 (OUTLIER) cc_final: 0.5412 (mt) REVERT: E 815 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7903 (mt) REVERT: E 848 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7457 (mmm) REVERT: E 878 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7668 (m-10) REVERT: E 1650 SER cc_start: 0.6186 (m) cc_final: 0.5963 (p) REVERT: F 189 GLU cc_start: 0.4464 (mt-10) cc_final: 0.4117 (mt-10) REVERT: F 207 MET cc_start: 0.1500 (tmm) cc_final: -0.0260 (mtt) REVERT: F 384 MET cc_start: 0.2343 (ppp) cc_final: 0.2128 (ppp) REVERT: F 398 MET cc_start: 0.2706 (mtt) cc_final: 0.2293 (ptp) REVERT: F 533 LEU cc_start: 0.0607 (OUTLIER) cc_final: 0.0028 (mt) REVERT: F 745 ARG cc_start: 0.2967 (mtm-85) cc_final: 0.2763 (mtm-85) REVERT: F 1142 GLU cc_start: 0.3306 (OUTLIER) cc_final: 0.1887 (mm-30) REVERT: F 1195 PHE cc_start: 0.5152 (OUTLIER) cc_final: 0.3958 (m-10) REVERT: F 1196 SER cc_start: 0.6693 (t) cc_final: 0.6350 (m) REVERT: F 1363 ILE cc_start: 0.7001 (tp) cc_final: 0.6516 (tp) REVERT: I 657 GLN cc_start: 0.4637 (pp30) cc_final: 0.4148 (pp30) REVERT: I 661 LYS cc_start: 0.7190 (mmmt) cc_final: 0.6933 (mtpt) REVERT: I 678 GLN cc_start: 0.4335 (OUTLIER) cc_final: 0.4077 (tp-100) REVERT: J 303 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.7024 (pm20) REVERT: J 444 ILE cc_start: 0.5837 (OUTLIER) cc_final: 0.5319 (tp) REVERT: J 463 LYS cc_start: 0.7725 (mtmm) cc_final: 0.7509 (pttm) REVERT: K 414 LYS cc_start: 0.3389 (tttt) cc_final: 0.3065 (tptt) REVERT: K 518 ARG cc_start: 0.6610 (tmm-80) cc_final: 0.6153 (mmp-170) REVERT: L 685 MET cc_start: 0.5343 (mmp) cc_final: 0.4823 (mtt) REVERT: L 749 GLN cc_start: 0.4469 (mm-40) cc_final: 0.4121 (tp40) REVERT: L 799 SER cc_start: 0.7506 (OUTLIER) cc_final: 0.7088 (p) REVERT: L 823 LYS cc_start: 0.3931 (mtmm) cc_final: 0.3680 (pttm) REVERT: Z 80 PHE cc_start: 0.4798 (OUTLIER) cc_final: 0.4422 (m-80) REVERT: Z 122 LEU cc_start: 0.4116 (OUTLIER) cc_final: 0.2808 (pp) REVERT: Z 294 MET cc_start: 0.2020 (tmm) cc_final: -0.0818 (ptt) REVERT: Z 459 LEU cc_start: 0.6048 (tp) cc_final: 0.5508 (tt) REVERT: Z 716 LEU cc_start: 0.7972 (pp) cc_final: 0.7648 (pp) REVERT: Z 785 MET cc_start: 0.5310 (tpp) cc_final: 0.4987 (tpp) outliers start: 207 outliers final: 149 residues processed: 705 average time/residue: 0.6219 time to fit residues: 772.4581 Evaluate side-chains 666 residues out of total 7900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 497 time to evaluate : 5.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 797 SER Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 900 ASP Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 1013 LYS Chi-restraints excluded: chain C residue 1387 HIS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 783 ASP Chi-restraints excluded: chain D residue 810 ILE Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 886 ASN Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 980 SER Chi-restraints excluded: chain D residue 1053 MET Chi-restraints excluded: chain D residue 1118 LEU Chi-restraints excluded: chain D residue 1161 MET Chi-restraints excluded: chain D residue 1329 ASP Chi-restraints excluded: chain D residue 1384 ILE Chi-restraints excluded: chain D residue 1408 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 254 SER Chi-restraints excluded: chain E residue 303 GLU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 323 TYR Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 699 GLU Chi-restraints excluded: chain E residue 719 ILE Chi-restraints excluded: chain E residue 764 LYS Chi-restraints excluded: chain E residue 771 LEU Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain E residue 795 ILE Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 848 MET Chi-restraints excluded: chain E residue 878 PHE Chi-restraints excluded: chain E residue 909 GLU Chi-restraints excluded: chain E residue 1012 VAL Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1079 VAL Chi-restraints excluded: chain E residue 1167 LEU Chi-restraints excluded: chain E residue 1211 ILE Chi-restraints excluded: chain E residue 1227 VAL Chi-restraints excluded: chain E residue 1297 LYS Chi-restraints excluded: chain E residue 1306 ASN Chi-restraints excluded: chain E residue 1340 PHE Chi-restraints excluded: chain E residue 1391 LEU Chi-restraints excluded: chain E residue 1453 ILE Chi-restraints excluded: chain E residue 1466 TYR Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 64 PHE Chi-restraints excluded: chain F residue 163 ASN Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 325 PHE Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 533 LEU Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 609 LEU Chi-restraints excluded: chain F residue 623 VAL Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 713 PHE Chi-restraints excluded: chain F residue 719 ILE Chi-restraints excluded: chain F residue 730 VAL Chi-restraints excluded: chain F residue 837 TYR Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 926 LEU Chi-restraints excluded: chain F residue 928 LEU Chi-restraints excluded: chain F residue 982 PHE Chi-restraints excluded: chain F residue 1056 LEU Chi-restraints excluded: chain F residue 1128 ASP Chi-restraints excluded: chain F residue 1139 ILE Chi-restraints excluded: chain F residue 1142 GLU Chi-restraints excluded: chain F residue 1144 VAL Chi-restraints excluded: chain F residue 1195 PHE Chi-restraints excluded: chain F residue 1208 GLU Chi-restraints excluded: chain F residue 1309 LEU Chi-restraints excluded: chain F residue 1313 ILE Chi-restraints excluded: chain F residue 1347 ILE Chi-restraints excluded: chain F residue 1373 ASP Chi-restraints excluded: chain F residue 1439 GLU Chi-restraints excluded: chain F residue 1472 GLU Chi-restraints excluded: chain F residue 1486 LEU Chi-restraints excluded: chain F residue 1503 THR Chi-restraints excluded: chain F residue 1526 ILE Chi-restraints excluded: chain F residue 1528 VAL Chi-restraints excluded: chain F residue 1543 LEU Chi-restraints excluded: chain F residue 1624 GLN Chi-restraints excluded: chain F residue 1629 LEU Chi-restraints excluded: chain F residue 1636 LEU Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 450 PHE Chi-restraints excluded: chain H residue 402 GLN Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain I residue 678 GLN Chi-restraints excluded: chain I residue 712 ASP Chi-restraints excluded: chain I residue 764 SER Chi-restraints excluded: chain I residue 771 ASN Chi-restraints excluded: chain I residue 821 ILE Chi-restraints excluded: chain I residue 823 LYS Chi-restraints excluded: chain J residue 303 GLU Chi-restraints excluded: chain J residue 368 ASP Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 384 LEU Chi-restraints excluded: chain J residue 411 ASN Chi-restraints excluded: chain J residue 434 THR Chi-restraints excluded: chain J residue 444 ILE Chi-restraints excluded: chain K residue 353 TYR Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain K residue 448 GLU Chi-restraints excluded: chain L residue 745 TYR Chi-restraints excluded: chain L residue 771 ASN Chi-restraints excluded: chain L residue 793 LEU Chi-restraints excluded: chain L residue 799 SER Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 80 PHE Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 116 LYS Chi-restraints excluded: chain Z residue 119 GLU Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 122 LEU Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 139 PHE Chi-restraints excluded: chain Z residue 140 ILE Chi-restraints excluded: chain Z residue 234 ILE Chi-restraints excluded: chain Z residue 440 LEU Chi-restraints excluded: chain Z residue 514 LYS Chi-restraints excluded: chain Z residue 588 VAL Chi-restraints excluded: chain Z residue 589 LEU Chi-restraints excluded: chain Z residue 630 ARG Chi-restraints excluded: chain Z residue 637 ILE Chi-restraints excluded: chain Z residue 652 ILE Chi-restraints excluded: chain Z residue 675 VAL Chi-restraints excluded: chain Z residue 686 VAL Chi-restraints excluded: chain Z residue 708 VAL Chi-restraints excluded: chain Z residue 776 ILE Chi-restraints excluded: chain Z residue 804 ASP Chi-restraints excluded: chain Z residue 808 ASN Chi-restraints excluded: chain Z residue 824 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 768 optimal weight: 10.0000 chunk 506 optimal weight: 10.0000 chunk 815 optimal weight: 2.9990 chunk 497 optimal weight: 4.9990 chunk 387 optimal weight: 4.9990 chunk 567 optimal weight: 0.5980 chunk 855 optimal weight: 5.9990 chunk 787 optimal weight: 20.0000 chunk 681 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 526 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 488 GLN D 698 ASN ** D 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1492 HIS ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 GLN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 539 ASN ** F 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 720 HIS ** F 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1027 GLN F1202 ASN ** G 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 402 GLN ** I 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 691 ASN I 709 ASN ** J 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 418 GLN K 503 ASN L 654 HIS ** L 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 563 ASN ** Z 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4737 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 68075 Z= 0.295 Angle : 0.807 18.315 92300 Z= 0.409 Chirality : 0.046 0.283 10884 Planarity : 0.005 0.155 11817 Dihedral : 6.331 102.203 9215 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.27 % Favored : 90.40 % Rotamer: Outliers : 2.87 % Allowed : 21.30 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.05 % Twisted Proline : 0.86 % Twisted General : 0.08 % 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: -0.85 (0.09), residues: 8584 helix: 0.47 (0.07), residues: 5096 sheet: 0.21 (0.27), residues: 380 loop : -2.45 (0.11), residues: 3108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP H 335 HIS 0.013 0.001 HIS E1429 PHE 0.068 0.002 PHE F 572 TYR 0.069 0.002 TYR F1156 ARG 0.022 0.001 ARG F1247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17168 Ramachandran restraints generated. 8584 Oldfield, 0 Emsley, 8584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 7900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 501 time to evaluate : 5.817 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: A 501 MET cc_start: 0.2295 (ppp) cc_final: 0.1967 (ppp) REVERT: A 739 MET cc_start: 0.3076 (ptt) cc_final: 0.2808 (mtm) REVERT: A 819 MET cc_start: 0.0255 (mtp) cc_final: -0.3156 (mmm) REVERT: C 388 MET cc_start: -0.0836 (mmm) cc_final: -0.2200 (ptm) REVERT: C 861 GLN cc_start: 0.5426 (tt0) cc_final: 0.4890 (mm-40) REVERT: C 1104 LYS cc_start: 0.1893 (tttt) cc_final: 0.1469 (mmmt) REVERT: C 1289 MET cc_start: 0.1254 (tpp) cc_final: 0.0792 (tpp) REVERT: C 1310 MET cc_start: -0.0812 (mmt) cc_final: -0.1107 (mpp) REVERT: C 1387 HIS cc_start: 0.5238 (OUTLIER) cc_final: 0.4635 (t70) REVERT: D 199 ASN cc_start: 0.4129 (m-40) cc_final: 0.3261 (t0) REVERT: D 207 MET cc_start: 0.2627 (mmt) cc_final: 0.1047 (mmm) REVERT: D 327 MET cc_start: 0.1005 (mmm) cc_final: 0.0740 (ttt) REVERT: D 586 LEU cc_start: -0.1003 (OUTLIER) cc_final: -0.1372 (tt) REVERT: D 1349 MET cc_start: 0.3784 (mmp) cc_final: 0.3140 (mmp) REVERT: E 321 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7008 (tt) REVERT: E 457 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6630 (mp) REVERT: E 648 ARG cc_start: 0.7134 (mtt90) cc_final: 0.5954 (ptp-170) REVERT: E 764 LYS cc_start: 0.6537 (OUTLIER) cc_final: 0.6171 (ttmm) REVERT: E 771 LEU cc_start: 0.6355 (OUTLIER) cc_final: 0.5630 (mt) REVERT: E 878 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7568 (m-10) REVERT: E 1650 SER cc_start: 0.6359 (m) cc_final: 0.6084 (p) REVERT: F 384 MET cc_start: 0.2397 (ppp) cc_final: 0.1793 (ppp) REVERT: F 398 MET cc_start: 0.2877 (mtt) cc_final: 0.2283 (ptp) REVERT: F 533 LEU cc_start: 0.1011 (OUTLIER) cc_final: 0.0250 (mt) REVERT: F 845 ASP cc_start: 0.7740 (t0) cc_final: 0.7243 (t70) REVERT: F 1027 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: F 1142 GLU cc_start: 0.3428 (OUTLIER) cc_final: 0.2079 (mt-10) REVERT: F 1195 PHE cc_start: 0.5224 (OUTLIER) cc_final: 0.4030 (m-10) REVERT: F 1309 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.6327 (mt) REVERT: F 1373 ASP cc_start: 0.6673 (OUTLIER) cc_final: 0.5619 (t0) REVERT: F 1382 TYR cc_start: 0.4876 (t80) cc_final: 0.4273 (t80) REVERT: G 284 ILE cc_start: 0.3139 (mt) cc_final: 0.2895 (mt) REVERT: H 445 GLN cc_start: 0.9156 (tm-30) cc_final: 0.8919 (tm-30) REVERT: J 303 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7085 (pm20) REVERT: J 444 ILE cc_start: 0.5811 (OUTLIER) cc_final: 0.5311 (tp) REVERT: K 414 LYS cc_start: 0.3823 (tttt) cc_final: 0.3522 (tptt) REVERT: L 685 MET cc_start: 0.5370 (mmp) cc_final: 0.4990 (mtt) REVERT: L 799 SER cc_start: 0.7648 (OUTLIER) cc_final: 0.7241 (p) REVERT: L 823 LYS cc_start: 0.4336 (mtmm) cc_final: 0.4033 (pttm) REVERT: Z 80 PHE cc_start: 0.4891 (OUTLIER) cc_final: 0.4538 (m-80) REVERT: Z 122 LEU cc_start: 0.4468 (OUTLIER) cc_final: 0.4007 (tp) REVERT: Z 294 MET cc_start: 0.2076 (tmm) cc_final: 0.1827 (tpt) REVERT: Z 459 LEU cc_start: 0.6238 (tp) cc_final: 0.5654 (tt) REVERT: Z 464 ASN cc_start: 0.7929 (m110) cc_final: 0.7505 (p0) REVERT: Z 646 LEU cc_start: 0.6482 (mm) cc_final: 0.6231 (tp) REVERT: Z 716 LEU cc_start: 0.8071 (pp) cc_final: 0.7720 (pp) outliers start: 208 outliers final: 161 residues processed: 666 average time/residue: 0.6033 time to fit residues: 710.2796 Evaluate side-chains 654 residues out of total 7900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 475 time to evaluate : 5.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain C residue 117 TYR Chi-restraints excluded: chain C residue 495 THR Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 900 ASP Chi-restraints excluded: chain C residue 958 ASN Chi-restraints excluded: chain C residue 1013 LYS Chi-restraints excluded: chain C residue 1387 HIS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 783 ASP Chi-restraints excluded: chain D residue 810 ILE Chi-restraints excluded: chain D residue 828 ILE Chi-restraints excluded: chain D residue 886 ASN Chi-restraints excluded: chain D residue 936 VAL Chi-restraints excluded: chain D residue 980 SER Chi-restraints excluded: chain D residue 1118 LEU Chi-restraints excluded: chain D residue 1161 MET Chi-restraints excluded: chain D residue 1384 ILE Chi-restraints excluded: chain D residue 1408 VAL Chi-restraints excluded: chain D residue 1421 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 303 GLU Chi-restraints excluded: chain E residue 321 ILE Chi-restraints excluded: chain E residue 323 TYR Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 364 THR Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 457 LEU Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 598 VAL Chi-restraints excluded: chain E residue 601 VAL Chi-restraints excluded: chain E residue 602 VAL Chi-restraints excluded: chain E residue 641 ILE Chi-restraints excluded: chain E residue 662 THR Chi-restraints excluded: chain E residue 671 LEU Chi-restraints excluded: chain E residue 694 ILE Chi-restraints excluded: chain E residue 699 GLU Chi-restraints excluded: chain E residue 719 ILE Chi-restraints excluded: chain E residue 764 LYS Chi-restraints excluded: chain E residue 771 LEU Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain E residue 795 ILE Chi-restraints excluded: chain E residue 815 LEU Chi-restraints excluded: chain E residue 825 ILE Chi-restraints excluded: chain E residue 830 THR Chi-restraints excluded: chain E residue 848 MET Chi-restraints excluded: chain E residue 878 PHE Chi-restraints excluded: chain E residue 909 GLU Chi-restraints excluded: chain E residue 919 LEU Chi-restraints excluded: chain E residue 1012 VAL Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1025 ASN Chi-restraints excluded: chain E residue 1079 VAL Chi-restraints excluded: chain E residue 1167 LEU Chi-restraints excluded: chain E residue 1197 VAL Chi-restraints excluded: chain E residue 1211 ILE Chi-restraints excluded: chain E residue 1227 VAL Chi-restraints excluded: chain E residue 1297 LYS Chi-restraints excluded: chain E residue 1306 ASN Chi-restraints excluded: chain E residue 1391 LEU Chi-restraints excluded: chain E residue 1453 ILE Chi-restraints excluded: chain E residue 1463 SER Chi-restraints excluded: chain E residue 1466 TYR Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 163 ASN Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 356 ILE Chi-restraints excluded: chain F residue 416 TYR Chi-restraints excluded: chain F residue 533 LEU Chi-restraints excluded: chain F residue 606 VAL Chi-restraints excluded: chain F residue 609 LEU Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 713 PHE Chi-restraints excluded: chain F residue 719 ILE Chi-restraints excluded: chain F residue 781 LEU Chi-restraints excluded: chain F residue 786 THR Chi-restraints excluded: chain F residue 837 TYR Chi-restraints excluded: chain F residue 844 VAL Chi-restraints excluded: chain F residue 926 LEU Chi-restraints excluded: chain F residue 928 LEU Chi-restraints excluded: chain F residue 982 PHE Chi-restraints excluded: chain F residue 995 VAL Chi-restraints excluded: chain F residue 1027 GLN Chi-restraints excluded: chain F residue 1041 PHE Chi-restraints excluded: chain F residue 1056 LEU Chi-restraints excluded: chain F residue 1128 ASP Chi-restraints excluded: chain F residue 1131 THR Chi-restraints excluded: chain F residue 1139 ILE Chi-restraints excluded: chain F residue 1142 GLU Chi-restraints excluded: chain F residue 1144 VAL Chi-restraints excluded: chain F residue 1195 PHE Chi-restraints excluded: chain F residue 1208 GLU Chi-restraints excluded: chain F residue 1309 LEU Chi-restraints excluded: chain F residue 1313 ILE Chi-restraints excluded: chain F residue 1373 ASP Chi-restraints excluded: chain F residue 1439 GLU Chi-restraints excluded: chain F residue 1472 GLU Chi-restraints excluded: chain F residue 1486 LEU Chi-restraints excluded: chain F residue 1503 THR Chi-restraints excluded: chain F residue 1526 ILE Chi-restraints excluded: chain F residue 1528 VAL Chi-restraints excluded: chain F residue 1543 LEU Chi-restraints excluded: chain F residue 1624 GLN Chi-restraints excluded: chain F residue 1629 LEU Chi-restraints excluded: chain F residue 1636 LEU Chi-restraints excluded: chain F residue 1637 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 450 PHE Chi-restraints excluded: chain H residue 402 GLN Chi-restraints excluded: chain H residue 466 LEU Chi-restraints excluded: chain H residue 512 ILE Chi-restraints excluded: chain I residue 654 HIS Chi-restraints excluded: chain I residue 712 ASP Chi-restraints excluded: chain I residue 764 SER Chi-restraints excluded: chain I residue 771 ASN Chi-restraints excluded: chain I residue 821 ILE Chi-restraints excluded: chain I residue 823 LYS Chi-restraints excluded: chain J residue 303 GLU Chi-restraints excluded: chain J residue 375 LYS Chi-restraints excluded: chain J residue 380 TYR Chi-restraints excluded: chain J residue 384 LEU Chi-restraints excluded: chain J residue 411 ASN Chi-restraints excluded: chain J residue 434 THR Chi-restraints excluded: chain J residue 444 ILE Chi-restraints excluded: chain K residue 299 TRP Chi-restraints excluded: chain K residue 353 TYR Chi-restraints excluded: chain K residue 393 ASP Chi-restraints excluded: chain K residue 398 ILE Chi-restraints excluded: chain K residue 448 GLU Chi-restraints excluded: chain L residue 745 TYR Chi-restraints excluded: chain L residue 793 LEU Chi-restraints excluded: chain L residue 799 SER Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain Z residue 80 PHE Chi-restraints excluded: chain Z residue 92 THR Chi-restraints excluded: chain Z residue 116 LYS Chi-restraints excluded: chain Z residue 119 GLU Chi-restraints excluded: chain Z residue 121 ILE Chi-restraints excluded: chain Z residue 122 LEU Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 139 PHE Chi-restraints excluded: chain Z residue 140 ILE Chi-restraints excluded: chain Z residue 234 ILE Chi-restraints excluded: chain Z residue 440 LEU Chi-restraints excluded: chain Z residue 514 LYS Chi-restraints excluded: chain Z residue 554 VAL Chi-restraints excluded: chain Z residue 588 VAL Chi-restraints excluded: chain Z residue 589 LEU Chi-restraints excluded: chain Z residue 630 ARG Chi-restraints excluded: chain Z residue 637 ILE Chi-restraints excluded: chain Z residue 675 VAL Chi-restraints excluded: chain Z residue 686 VAL Chi-restraints excluded: chain Z residue 708 VAL Chi-restraints excluded: chain Z residue 776 ILE Chi-restraints excluded: chain Z residue 804 ASP Chi-restraints excluded: chain Z residue 808 ASN Chi-restraints excluded: chain Z residue 824 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 417 optimal weight: 0.8980 chunk 541 optimal weight: 9.9990 chunk 725 optimal weight: 9.9990 chunk 208 optimal weight: 20.0000 chunk 628 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 682 optimal weight: 3.9990 chunk 285 optimal weight: 10.0000 chunk 700 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1143 GLN ** E1153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1492 HIS ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 861 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 365 GLN I 678 GLN I 690 GLN ** J 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 418 GLN L 654 HIS ** L 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 227 GLN ** Z 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5364 r_free = 0.5364 target = 0.256368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.5208 r_free = 0.5208 target = 0.240590 restraints weight = 171879.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5184 r_free = 0.5184 target = 0.237818 restraints weight = 209485.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5171 r_free = 0.5171 target = 0.236707 restraints weight = 184258.498| |-----------------------------------------------------------------------------| r_work (final): 0.5152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4575 moved from start: 0.6239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 68075 Z= 0.319 Angle : 0.825 16.685 92300 Z= 0.419 Chirality : 0.047 0.331 10884 Planarity : 0.005 0.155 11817 Dihedral : 6.432 108.018 9211 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.20 % Favored : 90.51 % Rotamer: Outliers : 2.93 % Allowed : 21.35 % Favored : 75.72 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.05 % Twisted Proline : 1.29 % Twisted General : 0.07 % 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: -0.93 (0.09), residues: 8584 helix: 0.39 (0.07), residues: 5071 sheet: 0.28 (0.27), residues: 379 loop : -2.46 (0.11), residues: 3134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E1495 HIS 0.012 0.001 HIS E1429 PHE 0.066 0.002 PHE F 572 TYR 0.069 0.002 TYR F1156 ARG 0.013 0.001 ARG F 771 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15410.47 seconds wall clock time: 269 minutes 13.01 seconds (16153.01 seconds total)