Starting phenix.real_space_refine on Thu Jan 23 00:39:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2h_38010/01_2025/8x2h_38010.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2h_38010/01_2025/8x2h_38010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x2h_38010/01_2025/8x2h_38010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2h_38010/01_2025/8x2h_38010.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2h_38010/01_2025/8x2h_38010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2h_38010/01_2025/8x2h_38010.cif" } resolution = 2.9 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= 0.000 sd= 0.052 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 47 5.16 5 C 12219 2.51 5 N 3035 2.21 5 O 3786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 269 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 19088 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 19087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2363, 19087 Classifications: {'peptide': 2363} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 2306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5700 SG CYS A 698 46.893 50.407 184.224 1.00 66.12 S Time building chain proxies: 10.46, per 1000 atoms: 0.55 Number of scatterers: 19088 At special positions: 0 Unit cell: (97.83, 140.223, 223.922, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 47 16.00 O 3786 8.00 N 3035 7.00 C 12219 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: 4.32 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3000 " pdb="ZN ZN A3000 " - pdb=" SG CYS A 698 " pdb="ZN ZN A3000 " - pdb=" ND1 HIS A 653 " 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4462 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 43 sheets defined 27.9% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.32 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 21 through 34 Processing helix chain 'A' and resid 41 through 61 Processing helix chain 'A' and resid 68 through 90 removed outlier: 3.983A pdb=" N LYS A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A 85 " --> pdb=" O MET A 81 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 119 removed outlier: 3.623A pdb=" N ILE A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLN A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 148 removed outlier: 3.501A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.907A pdb=" N SER A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 194 removed outlier: 4.252A pdb=" N GLU A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.500A pdb=" N ILE A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 251 through 261 removed outlier: 3.544A pdb=" N GLU A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 324 removed outlier: 3.619A pdb=" N TYR A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 removed outlier: 4.028A pdb=" N ASP A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N MET A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 332 through 337' Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 394 through 421 removed outlier: 3.826A pdb=" N LEU A 398 " --> pdb=" O TYR A 394 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) Proline residue: A 416 - end of helix Processing helix chain 'A' and resid 423 through 436 Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 451 through 456 removed outlier: 4.638A pdb=" N LEU A 454 " --> pdb=" O THR A 451 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 456 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 483 removed outlier: 3.783A pdb=" N TYR A 474 " --> pdb=" O GLY A 470 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 475 " --> pdb=" O PRO A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.631A pdb=" N PHE A 501 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU A 502 " --> pdb=" O ARG A 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 498 through 502' Processing helix chain 'A' and resid 504 through 508 removed outlier: 4.039A pdb=" N ILE A 508 " --> pdb=" O LYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 519 Processing helix chain 'A' and resid 526 through 537 Processing helix chain 'A' and resid 558 through 568 Processing helix chain 'A' and resid 587 through 601 removed outlier: 3.764A pdb=" N TYR A 591 " --> pdb=" O ASP A 587 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 removed outlier: 3.546A pdb=" N ILE A 640 " --> pdb=" O PRO A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 683 Processing helix chain 'A' and resid 710 through 715 Processing helix chain 'A' and resid 715 through 720 Processing helix chain 'A' and resid 764 through 773 Processing helix chain 'A' and resid 793 through 808 removed outlier: 4.233A pdb=" N LEU A 797 " --> pdb=" O TYR A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 838 removed outlier: 3.639A pdb=" N LYS A 818 " --> pdb=" O ASP A 814 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS A 824 " --> pdb=" O MET A 820 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 826 " --> pdb=" O THR A 822 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN A 827 " --> pdb=" O GLU A 823 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A 838 " --> pdb=" O ARG A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 857 removed outlier: 3.764A pdb=" N SER A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 876 removed outlier: 3.999A pdb=" N LEU A 872 " --> pdb=" O SER A 868 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 934 Processing helix chain 'A' and resid 951 through 971 Processing helix chain 'A' and resid 975 through 980 Processing helix chain 'A' and resid 980 through 995 removed outlier: 3.768A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1017 removed outlier: 4.060A pdb=" N VAL A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1049 removed outlier: 3.659A pdb=" N SER A1049 " --> pdb=" O ILE A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1058 removed outlier: 3.619A pdb=" N GLN A1058 " --> pdb=" O LEU A1055 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1055 through 1058' Processing helix chain 'A' and resid 1059 through 1064 removed outlier: 3.517A pdb=" N ILE A1064 " --> pdb=" O ILE A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1081 removed outlier: 4.299A pdb=" N ILE A1078 " --> pdb=" O ALA A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1133 removed outlier: 4.160A pdb=" N ALA A1130 " --> pdb=" O HIS A1126 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLU A1131 " --> pdb=" O ILE A1127 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A1132 " --> pdb=" O SER A1128 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A1133 " --> pdb=" O LEU A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1206 removed outlier: 3.936A pdb=" N LEU A1206 " --> pdb=" O ILE A1202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1202 through 1206' Processing helix chain 'A' and resid 1245 through 1258 removed outlier: 3.601A pdb=" N TYR A1258 " --> pdb=" O ILE A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1311 removed outlier: 4.030A pdb=" N ARG A1309 " --> pdb=" O THR A1305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1352 removed outlier: 3.808A pdb=" N VAL A1352 " --> pdb=" O VAL A1348 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1348 through 1352' Processing helix chain 'A' and resid 1396 through 1399 Processing helix chain 'A' and resid 1432 through 1439 Processing helix chain 'A' and resid 1439 through 1450 Processing helix chain 'A' and resid 1558 through 1572 Processing helix chain 'A' and resid 1582 through 1587 Processing helix chain 'A' and resid 1588 through 1590 No H-bonds generated for 'chain 'A' and resid 1588 through 1590' Processing helix chain 'A' and resid 1680 through 1683 Processing helix chain 'A' and resid 1792 through 1800 Processing helix chain 'A' and resid 1868 through 1872 removed outlier: 3.584A pdb=" N LYS A1871 " --> pdb=" O ASP A1868 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER A1872 " --> pdb=" O PRO A1869 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1868 through 1872' Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 130 removed outlier: 6.152A pdb=" N LEU A 98 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE A 130 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE A 100 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN A 97 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU A 285 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N HIS A 99 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 381 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 376 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N GLN A 385 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 11.806A pdb=" N LYS A 374 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 578 through 583 removed outlier: 6.796A pdb=" N ILE A 646 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASN A 694 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU A 648 " --> pdb=" O ASN A 694 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N LEU A 696 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE A 650 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 691 " --> pdb=" O THR A 736 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 606 through 607 Processing sheet with id=AA5, first strand: chain 'A' and resid 744 through 746 Processing sheet with id=AA6, first strand: chain 'A' and resid 778 through 781 removed outlier: 3.742A pdb=" N LYS A 786 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 882 through 891 removed outlier: 9.901A pdb=" N PHE A 886 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N ILE A 901 " --> pdb=" O PHE A 886 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ASP A 888 " --> pdb=" O ARG A 899 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 899 " --> pdb=" O ASP A 888 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 936 through 939 removed outlier: 3.745A pdb=" N ASP A 938 " --> pdb=" O VAL A 945 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1066 through 1067 removed outlier: 4.165A pdb=" N ILE A1516 " --> pdb=" O ILE A1528 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A1528 " --> pdb=" O ILE A1516 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE A1518 " --> pdb=" O LEU A1526 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A1526 " --> pdb=" O ILE A1518 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASN A1520 " --> pdb=" O VAL A1524 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A1524 " --> pdb=" O ASN A1520 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE A1550 " --> pdb=" O ILE A1606 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASP A1608 " --> pdb=" O ILE A1550 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LEU A1552 " --> pdb=" O ASP A1608 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN A1610 " --> pdb=" O LEU A1552 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLY A1554 " --> pdb=" O ASN A1610 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE A1612 " --> pdb=" O GLY A1554 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N TYR A1556 " --> pdb=" O ILE A1612 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER A1614 " --> pdb=" O TYR A1556 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A1625 " --> pdb=" O PRO A1634 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1105 through 1107 Processing sheet with id=AB2, first strand: chain 'A' and resid 1136 through 1139 Processing sheet with id=AB3, first strand: chain 'A' and resid 1161 through 1164 removed outlier: 7.261A pdb=" N SER A1161 " --> pdb=" O ILE A1155 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE A1155 " --> pdb=" O SER A1161 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR A1163 " --> pdb=" O SER A1153 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER A1153 " --> pdb=" O ARG A1288 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ASN A1290 " --> pdb=" O SER A1153 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE A1155 " --> pdb=" O ASN A1290 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A1334 " --> pdb=" O ASN A1390 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N TYR A1392 " --> pdb=" O ILE A1334 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU A1336 " --> pdb=" O TYR A1392 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1179 through 1181 removed outlier: 6.638A pdb=" N ASP A1185 " --> pdb=" O PHE A1267 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ILE A1275 " --> pdb=" O GLY A1235 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLY A1235 " --> pdb=" O ILE A1275 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LYS A1277 " --> pdb=" O GLU A1233 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN A1227 " --> pdb=" O GLU A1283 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU A1168 " --> pdb=" O PHE A1230 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N TYR A1232 " --> pdb=" O GLU A1168 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1171 through 1173 Processing sheet with id=AB6, first strand: chain 'A' and resid 1219 through 1221 removed outlier: 6.945A pdb=" N TYR A1323 " --> pdb=" O VAL A1345 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ASP A1347 " --> pdb=" O TYR A1323 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU A1325 " --> pdb=" O ASP A1347 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N TRP A1344 " --> pdb=" O SER A1403 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N THR A1405 " --> pdb=" O TRP A1344 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE A1346 " --> pdb=" O THR A1405 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N SER A1407 " --> pdb=" O ILE A1346 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE A1412 " --> pdb=" O ILE A1408 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1353 through 1358 removed outlier: 4.659A pdb=" N ASN A1354 " --> pdb=" O GLY A1365 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1459 through 1466 Processing sheet with id=AB9, first strand: chain 'A' and resid 1675 through 1678 removed outlier: 6.362A pdb=" N ILE A1675 " --> pdb=" O ASN A1704 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR A1706 " --> pdb=" O ILE A1675 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE A1677 " --> pdb=" O THR A1706 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1815 through 1819 Processing sheet with id=AC2, first strand: chain 'A' and resid 1835 through 1838 removed outlier: 3.697A pdb=" N LYS A1847 " --> pdb=" O ASN A1852 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN A1852 " --> pdb=" O LYS A1847 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1856 through 1860 Processing sheet with id=AC4, first strand: chain 'A' and resid 1878 through 1882 Processing sheet with id=AC5, first strand: chain 'A' and resid 1898 through 1902 removed outlier: 3.626A pdb=" N GLU A1922 " --> pdb=" O ALA A1910 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1928 through 1932 Processing sheet with id=AC7, first strand: chain 'A' and resid 1949 through 1952 Processing sheet with id=AC8, first strand: chain 'A' and resid 1969 through 1973 Processing sheet with id=AC9, first strand: chain 'A' and resid 1989 through 1993 Processing sheet with id=AD1, first strand: chain 'A' and resid 2010 through 2013 Processing sheet with id=AD2, first strand: chain 'A' and resid 2029 through 2033 Processing sheet with id=AD3, first strand: chain 'A' and resid 2059 through 2063 Processing sheet with id=AD4, first strand: chain 'A' and resid 2079 through 2082 Processing sheet with id=AD5, first strand: chain 'A' and resid 2101 through 2105 removed outlier: 4.008A pdb=" N TYR A2111 " --> pdb=" O GLN A2119 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 2121 through 2125 Processing sheet with id=AD7, first strand: chain 'A' and resid 2141 through 2145 removed outlier: 4.608A pdb=" N GLY A2141 " --> pdb=" O ILE A2152 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE A2152 " --> pdb=" O GLY A2141 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 2161 through 2163 removed outlier: 4.016A pdb=" N TYR A2171 " --> pdb=" O VAL A2187 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 2191 through 2195 removed outlier: 4.755A pdb=" N TYR A2201 " --> pdb=" O GLU A2209 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 2211 through 2215 Processing sheet with id=AE2, first strand: chain 'A' and resid 2232 through 2236 Processing sheet with id=AE3, first strand: chain 'A' and resid 2252 through 2256 Processing sheet with id=AE4, first strand: chain 'A' and resid 2272 through 2276 Processing sheet with id=AE5, first strand: chain 'A' and resid 2292 through 2296 Processing sheet with id=AE6, first strand: chain 'A' and resid 2322 through 2326 Processing sheet with id=AE7, first strand: chain 'A' and resid 2343 through 2346 removed outlier: 4.515A pdb=" N TYR A2352 " --> pdb=" O VAL A2361 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 1914 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: 13.47 Time building geometry restraints manager: 5.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3338 1.30 - 1.43: 5027 1.43 - 1.56: 11022 1.56 - 1.69: 0 1.69 - 1.82: 84 Bond restraints: 19471 Sorted by residual: bond pdb=" C TYR A1683 " pdb=" N GLY A1684 " ideal model delta sigma weight residual 1.331 1.252 0.078 1.46e-02 4.69e+03 2.86e+01 bond pdb=" C TYR A1683 " pdb=" O TYR A1683 " ideal model delta sigma weight residual 1.234 1.173 0.061 1.17e-02 7.31e+03 2.71e+01 bond pdb=" CA TYR A1683 " pdb=" CB TYR A1683 " ideal model delta sigma weight residual 1.530 1.500 0.031 1.62e-02 3.81e+03 3.62e+00 bond pdb=" CB TYR A1683 " pdb=" CG TYR A1683 " ideal model delta sigma weight residual 1.512 1.476 0.036 2.20e-02 2.07e+03 2.67e+00 bond pdb=" CA TYR A1683 " pdb=" C TYR A1683 " ideal model delta sigma weight residual 1.523 1.504 0.019 1.23e-02 6.61e+03 2.29e+00 ... (remaining 19466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 26284 4.84 - 9.68: 57 9.68 - 14.52: 1 14.52 - 19.36: 0 19.36 - 24.20: 1 Bond angle restraints: 26343 Sorted by residual: angle pdb=" C TYR A1683 " pdb=" CA TYR A1683 " pdb=" CB TYR A1683 " ideal model delta sigma weight residual 109.70 85.50 24.20 1.61e+00 3.86e-01 2.26e+02 angle pdb=" C VAL A1650 " pdb=" CA VAL A1650 " pdb=" CB VAL A1650 " ideal model delta sigma weight residual 110.88 103.75 7.13 1.09e+00 8.42e-01 4.28e+01 angle pdb=" CA TYR A1683 " pdb=" C TYR A1683 " pdb=" O TYR A1683 " ideal model delta sigma weight residual 121.15 128.07 -6.92 1.10e+00 8.26e-01 3.95e+01 angle pdb=" N VAL A 121 " pdb=" CA VAL A 121 " pdb=" C VAL A 121 " ideal model delta sigma weight residual 113.71 109.10 4.61 9.50e-01 1.11e+00 2.36e+01 angle pdb=" C TYR A 538 " pdb=" N PHE A 539 " pdb=" CA PHE A 539 " ideal model delta sigma weight residual 121.54 130.05 -8.51 1.91e+00 2.74e-01 1.98e+01 ... (remaining 26338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 9616 18.01 - 36.03: 1402 36.03 - 54.04: 477 54.04 - 72.05: 126 72.05 - 90.07: 36 Dihedral angle restraints: 11657 sinusoidal: 4688 harmonic: 6969 Sorted by residual: dihedral pdb=" CA SER A1774 " pdb=" C SER A1774 " pdb=" N ASP A1775 " pdb=" CA ASP A1775 " ideal model delta harmonic sigma weight residual 180.00 121.80 58.20 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" C TYR A1683 " pdb=" N TYR A1683 " pdb=" CA TYR A1683 " pdb=" CB TYR A1683 " ideal model delta harmonic sigma weight residual -122.60 -96.04 -26.56 0 2.50e+00 1.60e-01 1.13e+02 dihedral pdb=" CA ALA A1068 " pdb=" C ALA A1068 " pdb=" N VAL A1069 " pdb=" CA VAL A1069 " ideal model delta harmonic sigma weight residual -180.00 -147.47 -32.53 0 5.00e+00 4.00e-02 4.23e+01 ... (remaining 11654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2061 0.049 - 0.098: 645 0.098 - 0.147: 185 0.147 - 0.197: 12 0.197 - 0.246: 2 Chirality restraints: 2905 Sorted by residual: chirality pdb=" CA TYR A1683 " pdb=" N TYR A1683 " pdb=" C TYR A1683 " pdb=" CB TYR A1683 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ILE A 606 " pdb=" N ILE A 606 " pdb=" C ILE A 606 " pdb=" CB ILE A 606 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ILE A1637 " pdb=" N ILE A1637 " pdb=" C ILE A1637 " pdb=" CB ILE A1637 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.02e-01 ... (remaining 2902 not shown) Planarity restraints: 3406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 369 " 0.045 5.00e-02 4.00e+02 6.90e-02 7.61e+00 pdb=" N PRO A 370 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A1710 " -0.039 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO A1711 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A1711 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A1711 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1029 " 0.038 5.00e-02 4.00e+02 5.82e-02 5.43e+00 pdb=" N PRO A1030 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A1030 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A1030 " 0.031 5.00e-02 4.00e+02 ... (remaining 3403 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 307 2.61 - 3.18: 16759 3.18 - 3.75: 28844 3.75 - 4.33: 41204 4.33 - 4.90: 66285 Nonbonded interactions: 153399 Sorted by model distance: nonbonded pdb=" OH TYR A 125 " pdb=" O LEU A 363 " model vdw 2.037 3.040 nonbonded pdb=" ND2 ASN A2307 " pdb=" O ASN A2312 " model vdw 2.053 3.120 nonbonded pdb=" O ASN A 58 " pdb=" OG1 THR A 62 " model vdw 2.087 3.040 nonbonded pdb=" O SER A 90 " pdb=" OG SER A 90 " model vdw 2.096 3.040 nonbonded pdb=" O THR A1547 " pdb=" ND2 ASN A1597 " model vdw 2.097 3.120 ... (remaining 153394 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 53.070 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5644 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 19471 Z= 0.291 Angle : 0.846 24.195 26343 Z= 0.489 Chirality : 0.051 0.246 2905 Planarity : 0.005 0.069 3406 Dihedral : 20.155 90.067 7195 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.73 % Favored : 91.11 % Rotamer: Outliers : 13.38 % Allowed : 28.73 % Favored : 57.88 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.22 (0.14), residues: 2361 helix: -3.22 (0.15), residues: 622 sheet: -2.63 (0.22), residues: 411 loop : -2.68 (0.14), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1743 HIS 0.007 0.001 HIS A1178 PHE 0.034 0.002 PHE A 539 TYR 0.026 0.002 TYR A1531 ARG 0.009 0.001 ARG A1241 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 286 poor density : 212 time to evaluate : 2.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.6133 (mtm) cc_final: 0.5802 (mtm) REVERT: A 68 ARG cc_start: 0.5450 (OUTLIER) cc_final: 0.4885 (ptm160) REVERT: A 81 MET cc_start: 0.5487 (OUTLIER) cc_final: 0.5149 (ttt) REVERT: A 141 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.5998 (tp) REVERT: A 190 TYR cc_start: 0.4713 (OUTLIER) cc_final: 0.3729 (t80) REVERT: A 191 LYS cc_start: 0.7047 (mttt) cc_final: 0.6692 (mttt) REVERT: A 213 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.4129 (mp0) REVERT: A 262 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6628 (mmt90) REVERT: A 278 LYS cc_start: 0.6833 (OUTLIER) cc_final: 0.6459 (ttpt) REVERT: A 318 GLU cc_start: 0.4735 (OUTLIER) cc_final: 0.4389 (mt-10) REVERT: A 530 GLN cc_start: 0.5728 (OUTLIER) cc_final: 0.5276 (tp40) REVERT: A 573 ARG cc_start: 0.1339 (OUTLIER) cc_final: 0.0610 (ptt180) REVERT: A 576 GLU cc_start: 0.4972 (OUTLIER) cc_final: 0.3525 (pm20) REVERT: A 579 HIS cc_start: 0.1234 (OUTLIER) cc_final: 0.0692 (t-170) REVERT: A 642 ASN cc_start: 0.4202 (OUTLIER) cc_final: 0.3991 (p0) REVERT: A 769 ILE cc_start: 0.6363 (OUTLIER) cc_final: 0.6040 (mp) REVERT: A 820 MET cc_start: 0.4651 (tmm) cc_final: 0.4151 (tmm) REVERT: A 974 THR cc_start: 0.4437 (OUTLIER) cc_final: 0.3778 (p) REVERT: A 1019 ILE cc_start: 0.4792 (OUTLIER) cc_final: 0.4531 (tt) REVERT: A 1314 TYR cc_start: 0.5245 (OUTLIER) cc_final: 0.3407 (m-80) REVERT: A 1334 ILE cc_start: 0.3183 (OUTLIER) cc_final: 0.2386 (mp) REVERT: A 1342 ASP cc_start: 0.5625 (OUTLIER) cc_final: 0.5401 (t70) REVERT: A 1530 ASN cc_start: 0.6463 (OUTLIER) cc_final: 0.5601 (p0) REVERT: A 1663 HIS cc_start: 0.5846 (OUTLIER) cc_final: 0.4050 (p-80) REVERT: A 1735 ASN cc_start: 0.4117 (OUTLIER) cc_final: 0.3787 (m110) REVERT: A 1810 PHE cc_start: 0.4995 (p90) cc_final: 0.4738 (p90) REVERT: A 1822 ASP cc_start: 0.6502 (m-30) cc_final: 0.6131 (m-30) REVERT: A 1853 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7057 (tp) REVERT: A 1854 ILE cc_start: 0.5978 (OUTLIER) cc_final: 0.5731 (mt) REVERT: A 2003 ASP cc_start: 0.2102 (OUTLIER) cc_final: 0.1374 (m-30) REVERT: A 2265 GLU cc_start: 0.2446 (OUTLIER) cc_final: 0.2166 (tp30) REVERT: A 2273 TYR cc_start: 0.2225 (OUTLIER) cc_final: 0.1966 (t80) REVERT: A 2329 LYS cc_start: 0.3461 (OUTLIER) cc_final: 0.2514 (tptp) outliers start: 286 outliers final: 124 residues processed: 469 average time/residue: 0.9359 time to fit residues: 523.4569 Evaluate side-chains 309 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 157 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 576 GLU Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 769 ILE Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 875 GLN Chi-restraints excluded: chain A residue 885 SER Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1149 ASP Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1161 SER Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1281 ARG Chi-restraints excluded: chain A residue 1282 TYR Chi-restraints excluded: chain A residue 1314 TYR Chi-restraints excluded: chain A residue 1322 SER Chi-restraints excluded: chain A residue 1334 ILE Chi-restraints excluded: chain A residue 1342 ASP Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1467 ASN Chi-restraints excluded: chain A residue 1472 ASN Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain A residue 1485 THR Chi-restraints excluded: chain A residue 1530 ASN Chi-restraints excluded: chain A residue 1531 TYR Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1606 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1641 ILE Chi-restraints excluded: chain A residue 1644 THR Chi-restraints excluded: chain A residue 1645 SER Chi-restraints excluded: chain A residue 1663 HIS Chi-restraints excluded: chain A residue 1671 SER Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1702 GLU Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1715 CYS Chi-restraints excluded: chain A residue 1735 ASN Chi-restraints excluded: chain A residue 1736 ASP Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1774 SER Chi-restraints excluded: chain A residue 1780 LYS Chi-restraints excluded: chain A residue 1792 SER Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1843 LEU Chi-restraints excluded: chain A residue 1853 LEU Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain A residue 1902 THR Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1948 GLU Chi-restraints excluded: chain A residue 1960 ASN Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 2003 ASP Chi-restraints excluded: chain A residue 2013 VAL Chi-restraints excluded: chain A residue 2028 LEU Chi-restraints excluded: chain A residue 2087 SER Chi-restraints excluded: chain A residue 2088 THR Chi-restraints excluded: chain A residue 2144 ASN Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2194 ARG Chi-restraints excluded: chain A residue 2230 TYR Chi-restraints excluded: chain A residue 2236 VAL Chi-restraints excluded: chain A residue 2251 THR Chi-restraints excluded: chain A residue 2265 GLU Chi-restraints excluded: chain A residue 2270 GLN Chi-restraints excluded: chain A residue 2273 TYR Chi-restraints excluded: chain A residue 2280 MET Chi-restraints excluded: chain A residue 2321 THR Chi-restraints excluded: chain A residue 2329 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.8980 chunk 178 optimal weight: 0.1980 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 120 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 214 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 10 GLN A 20 GLN A 35 HIS A 36 ASN A 212 ASN A 294 GLN A 343 GLN A 379 ASN A 405 ASN A 479 GLN A 510 GLN A 553 GLN A 579 HIS ** A 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN A 639 GLN A 659 ASN A 846 ASN A 853 ASN ** A1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 GLN A1294 ASN ** A1307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1370 ASN A1456 HIS A1504 ASN A1520 ASN A1530 ASN A1735 ASN A1763 GLN A1840 ASN ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1925 ASN A2058 ASN A2176 ASN A2196 ASN A2234 ASN A2312 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5217 r_free = 0.5217 target = 0.247228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.208131 restraints weight = 24418.564| |-----------------------------------------------------------------------------| r_work (start): 0.4878 rms_B_bonded: 3.31 r_work: 0.4522 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19471 Z= 0.194 Angle : 0.687 10.104 26343 Z= 0.364 Chirality : 0.048 0.192 2905 Planarity : 0.004 0.056 3406 Dihedral : 11.487 64.019 2832 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.07 % Favored : 92.84 % Rotamer: Outliers : 9.45 % Allowed : 30.60 % Favored : 59.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.12 (0.15), residues: 2361 helix: -1.81 (0.18), residues: 634 sheet: -2.16 (0.23), residues: 416 loop : -2.19 (0.15), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1743 HIS 0.005 0.001 HIS A1178 PHE 0.029 0.002 PHE A 539 TYR 0.020 0.001 TYR A1531 ARG 0.004 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 168 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.7023 (mt0) REVERT: A 68 ARG cc_start: 0.5724 (OUTLIER) cc_final: 0.4979 (ptp-170) REVERT: A 81 MET cc_start: 0.5999 (ttp) cc_final: 0.5783 (ttt) REVERT: A 134 ASN cc_start: 0.7220 (OUTLIER) cc_final: 0.6964 (t0) REVERT: A 161 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6707 (tp) REVERT: A 190 TYR cc_start: 0.4896 (OUTLIER) cc_final: 0.3937 (t80) REVERT: A 191 LYS cc_start: 0.6578 (mttt) cc_final: 0.6352 (mttt) REVERT: A 278 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6810 (ttpt) REVERT: A 573 ARG cc_start: 0.1480 (OUTLIER) cc_final: -0.0247 (ptt180) REVERT: A 639 GLN cc_start: 0.6110 (OUTLIER) cc_final: 0.5632 (pm20) REVERT: A 642 ASN cc_start: 0.5056 (OUTLIER) cc_final: 0.4397 (p0) REVERT: A 820 MET cc_start: 0.5270 (tmm) cc_final: 0.4926 (tmm) REVERT: A 832 ILE cc_start: 0.5332 (OUTLIER) cc_final: 0.4889 (pt) REVERT: A 1019 ILE cc_start: 0.5041 (OUTLIER) cc_final: 0.4576 (tt) REVERT: A 1058 GLN cc_start: 0.7155 (pt0) cc_final: 0.6304 (mm-40) REVERT: A 1092 LEU cc_start: 0.1143 (OUTLIER) cc_final: 0.0756 (tt) REVERT: A 1145 MET cc_start: 0.5337 (ttp) cc_final: 0.4867 (ttt) REVERT: A 1270 ILE cc_start: 0.6156 (OUTLIER) cc_final: 0.5828 (pp) REVERT: A 1342 ASP cc_start: 0.5500 (OUTLIER) cc_final: 0.4922 (t70) REVERT: A 1472 ASN cc_start: 0.6406 (OUTLIER) cc_final: 0.5906 (m-40) REVERT: A 1483 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6270 (tp) REVERT: A 1613 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.6381 (tt) REVERT: A 1663 HIS cc_start: 0.5565 (OUTLIER) cc_final: 0.3557 (p-80) REVERT: A 1703 ILE cc_start: 0.6170 (OUTLIER) cc_final: 0.5833 (mt) REVERT: A 1822 ASP cc_start: 0.5897 (m-30) cc_final: 0.5506 (m-30) REVERT: A 1960 ASN cc_start: 0.5878 (OUTLIER) cc_final: 0.5677 (p0) REVERT: A 1988 THR cc_start: 0.4105 (OUTLIER) cc_final: 0.3878 (t) REVERT: A 2038 LYS cc_start: 0.3321 (mmtp) cc_final: 0.3110 (mmtp) REVERT: A 2298 ASP cc_start: 0.0152 (OUTLIER) cc_final: -0.0189 (p0) REVERT: A 2329 LYS cc_start: 0.3038 (OUTLIER) cc_final: 0.2655 (tptp) outliers start: 202 outliers final: 79 residues processed: 346 average time/residue: 0.9662 time to fit residues: 396.7509 Evaluate side-chains 248 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 146 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 8 GLN Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1281 ARG Chi-restraints excluded: chain A residue 1282 TYR Chi-restraints excluded: chain A residue 1342 ASP Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1467 ASN Chi-restraints excluded: chain A residue 1472 ASN Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain A residue 1485 THR Chi-restraints excluded: chain A residue 1530 ASN Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1603 ILE Chi-restraints excluded: chain A residue 1606 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1617 ASN Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1663 HIS Chi-restraints excluded: chain A residue 1671 SER Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1703 ILE Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1715 CYS Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1774 SER Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1860 ILE Chi-restraints excluded: chain A residue 1899 VAL Chi-restraints excluded: chain A residue 1902 THR Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1948 GLU Chi-restraints excluded: chain A residue 1960 ASN Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1988 THR Chi-restraints excluded: chain A residue 2013 VAL Chi-restraints excluded: chain A residue 2088 THR Chi-restraints excluded: chain A residue 2104 VAL Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2194 ARG Chi-restraints excluded: chain A residue 2230 TYR Chi-restraints excluded: chain A residue 2270 GLN Chi-restraints excluded: chain A residue 2273 TYR Chi-restraints excluded: chain A residue 2280 MET Chi-restraints excluded: chain A residue 2298 ASP Chi-restraints excluded: chain A residue 2329 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 225 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 234 optimal weight: 30.0000 chunk 116 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 177 optimal weight: 0.2980 chunk 217 optimal weight: 9.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 10 GLN A 20 GLN ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 GLN ** A1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 ASN A1472 ASN ** A1590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1727 ASN A1763 GLN ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2002 ASN ** A2260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2306 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5183 r_free = 0.5183 target = 0.240997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.4737 r_free = 0.4737 target = 0.191835 restraints weight = 24630.397| |-----------------------------------------------------------------------------| r_work (start): 0.4675 rms_B_bonded: 2.04 r_work: 0.4508 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4418 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.4418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 19471 Z= 0.418 Angle : 0.864 12.842 26343 Z= 0.457 Chirality : 0.054 0.188 2905 Planarity : 0.005 0.067 3406 Dihedral : 10.415 61.550 2688 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.40 % Favored : 90.47 % Rotamer: Outliers : 11.56 % Allowed : 29.81 % Favored : 58.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.23 (0.15), residues: 2361 helix: -2.07 (0.17), residues: 636 sheet: -2.12 (0.24), residues: 422 loop : -2.20 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1743 HIS 0.004 0.001 HIS A1178 PHE 0.035 0.003 PHE A 539 TYR 0.030 0.003 TYR A1531 ARG 0.006 0.001 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 247 poor density : 146 time to evaluate : 2.257 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: A 68 ARG cc_start: 0.5746 (OUTLIER) cc_final: 0.4938 (ptp-170) REVERT: A 161 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6882 (tp) REVERT: A 190 TYR cc_start: 0.5550 (OUTLIER) cc_final: 0.4007 (t80) REVERT: A 404 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.7072 (ttpt) REVERT: A 415 ASN cc_start: 0.7015 (OUTLIER) cc_final: 0.6713 (t0) REVERT: A 507 LYS cc_start: 0.3193 (OUTLIER) cc_final: 0.2909 (mttp) REVERT: A 573 ARG cc_start: 0.1988 (OUTLIER) cc_final: 0.0263 (ptt180) REVERT: A 642 ASN cc_start: 0.5429 (OUTLIER) cc_final: 0.4904 (p0) REVERT: A 690 TYR cc_start: 0.4625 (OUTLIER) cc_final: 0.2562 (t80) REVERT: A 780 PHE cc_start: 0.5014 (OUTLIER) cc_final: 0.4167 (t80) REVERT: A 832 ILE cc_start: 0.5539 (OUTLIER) cc_final: 0.5186 (pt) REVERT: A 1058 GLN cc_start: 0.7311 (pt0) cc_final: 0.6470 (mm-40) REVERT: A 1145 MET cc_start: 0.5609 (ttp) cc_final: 0.5123 (ttt) REVERT: A 1164 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6275 (pp) REVERT: A 1270 ILE cc_start: 0.5978 (OUTLIER) cc_final: 0.5636 (pp) REVERT: A 1342 ASP cc_start: 0.5738 (OUTLIER) cc_final: 0.5142 (t70) REVERT: A 1364 LYS cc_start: 0.3165 (OUTLIER) cc_final: 0.2195 (mttt) REVERT: A 1701 ASP cc_start: 0.5971 (OUTLIER) cc_final: 0.5332 (p0) REVERT: A 1703 ILE cc_start: 0.6123 (OUTLIER) cc_final: 0.5910 (mt) REVERT: A 1854 ILE cc_start: 0.6549 (OUTLIER) cc_final: 0.6225 (mt) REVERT: A 1930 LEU cc_start: 0.3106 (OUTLIER) cc_final: 0.2363 (tp) REVERT: A 1959 PHE cc_start: 0.4796 (OUTLIER) cc_final: 0.4364 (m-80) REVERT: A 1985 ILE cc_start: 0.4405 (OUTLIER) cc_final: 0.4184 (mm) REVERT: A 1988 THR cc_start: 0.4440 (OUTLIER) cc_final: 0.4220 (t) REVERT: A 2216 GLU cc_start: 0.3637 (OUTLIER) cc_final: 0.3283 (tm-30) REVERT: A 2249 MET cc_start: 0.3830 (tpt) cc_final: 0.3521 (tpp) REVERT: A 2273 TYR cc_start: 0.4199 (OUTLIER) cc_final: 0.3772 (m-80) outliers start: 247 outliers final: 116 residues processed: 367 average time/residue: 0.9029 time to fit residues: 397.9476 Evaluate side-chains 276 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 136 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 257 GLN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 507 LYS Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 780 PHE Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 939 ASN Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1149 ASP Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1282 TYR Chi-restraints excluded: chain A residue 1342 ASP Chi-restraints excluded: chain A residue 1364 LYS Chi-restraints excluded: chain A residue 1377 ILE Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain A residue 1467 ASN Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain A residue 1485 THR Chi-restraints excluded: chain A residue 1492 SER Chi-restraints excluded: chain A residue 1530 ASN Chi-restraints excluded: chain A residue 1533 LYS Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1562 VAL Chi-restraints excluded: chain A residue 1606 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1665 ASP Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1701 ASP Chi-restraints excluded: chain A residue 1703 ILE Chi-restraints excluded: chain A residue 1706 THR Chi-restraints excluded: chain A residue 1738 SER Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1774 SER Chi-restraints excluded: chain A residue 1779 ASP Chi-restraints excluded: chain A residue 1790 ASP Chi-restraints excluded: chain A residue 1792 SER Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1859 THR Chi-restraints excluded: chain A residue 1860 ILE Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain A residue 1899 VAL Chi-restraints excluded: chain A residue 1902 THR Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1947 VAL Chi-restraints excluded: chain A residue 1948 GLU Chi-restraints excluded: chain A residue 1959 PHE Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 1988 THR Chi-restraints excluded: chain A residue 2008 VAL Chi-restraints excluded: chain A residue 2013 VAL Chi-restraints excluded: chain A residue 2054 LEU Chi-restraints excluded: chain A residue 2088 THR Chi-restraints excluded: chain A residue 2104 VAL Chi-restraints excluded: chain A residue 2127 ASP Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2216 GLU Chi-restraints excluded: chain A residue 2230 TYR Chi-restraints excluded: chain A residue 2273 TYR Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2298 ASP Chi-restraints excluded: chain A residue 2354 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 96 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 94 optimal weight: 0.0870 chunk 128 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN A 58 ASN A 553 GLN A1052 ASN A1257 HIS ** A1593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1892 GLN A2260 ASN ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2306 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5231 r_free = 0.5231 target = 0.247871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.213378 restraints weight = 24329.469| |-----------------------------------------------------------------------------| r_work (start): 0.4921 rms_B_bonded: 3.31 r_work: 0.4494 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6110 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19471 Z= 0.180 Angle : 0.650 10.298 26343 Z= 0.343 Chirality : 0.046 0.176 2905 Planarity : 0.004 0.052 3406 Dihedral : 8.816 59.316 2657 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.18 % Favored : 93.73 % Rotamer: Outliers : 7.53 % Allowed : 33.08 % Favored : 59.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.47 (0.16), residues: 2361 helix: -1.15 (0.19), residues: 643 sheet: -1.74 (0.24), residues: 425 loop : -1.86 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1743 HIS 0.004 0.001 HIS A1178 PHE 0.029 0.001 PHE A 539 TYR 0.032 0.001 TYR A 14 ARG 0.004 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 163 time to evaluate : 2.021 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: A 68 ARG cc_start: 0.5749 (OUTLIER) cc_final: 0.4888 (ptp-170) REVERT: A 81 MET cc_start: 0.6168 (OUTLIER) cc_final: 0.5857 (ttt) REVERT: A 159 GLU cc_start: 0.5436 (OUTLIER) cc_final: 0.4978 (pm20) REVERT: A 190 TYR cc_start: 0.5580 (OUTLIER) cc_final: 0.4046 (t80) REVERT: A 318 GLU cc_start: 0.4409 (OUTLIER) cc_final: 0.3778 (mp0) REVERT: A 404 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7177 (ttpt) REVERT: A 573 ARG cc_start: 0.1764 (OUTLIER) cc_final: -0.0994 (ptt180) REVERT: A 616 GLU cc_start: 0.5504 (OUTLIER) cc_final: 0.3901 (mp0) REVERT: A 832 ILE cc_start: 0.5252 (OUTLIER) cc_final: 0.4844 (pt) REVERT: A 974 THR cc_start: 0.3416 (OUTLIER) cc_final: 0.3104 (m) REVERT: A 1020 ASP cc_start: 0.5041 (OUTLIER) cc_final: 0.4626 (m-30) REVERT: A 1050 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7912 (tt0) REVERT: A 1229 VAL cc_start: 0.5017 (OUTLIER) cc_final: 0.4448 (p) REVERT: A 1325 LEU cc_start: 0.6455 (tp) cc_final: 0.6144 (tp) REVERT: A 1332 MET cc_start: 0.7429 (tpt) cc_final: 0.7111 (mmt) REVERT: A 1342 ASP cc_start: 0.5724 (OUTLIER) cc_final: 0.5200 (t70) REVERT: A 1421 VAL cc_start: 0.6932 (t) cc_final: 0.6460 (t) REVERT: A 1479 LYS cc_start: 0.6972 (tttm) cc_final: 0.6674 (pttp) REVERT: A 1483 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6238 (tp) REVERT: A 1702 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.5376 (tp30) REVERT: A 1822 ASP cc_start: 0.5612 (m-30) cc_final: 0.5093 (m-30) REVERT: A 1854 ILE cc_start: 0.6387 (OUTLIER) cc_final: 0.6134 (mt) REVERT: A 1927 ILE cc_start: 0.7137 (OUTLIER) cc_final: 0.6790 (pp) REVERT: A 1985 ILE cc_start: 0.4272 (OUTLIER) cc_final: 0.4071 (mm) REVERT: A 2273 TYR cc_start: 0.4154 (OUTLIER) cc_final: 0.3445 (t80) REVERT: A 2274 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.6790 (pt) REVERT: A 2298 ASP cc_start: 0.0542 (OUTLIER) cc_final: 0.0090 (p0) outliers start: 161 outliers final: 75 residues processed: 304 average time/residue: 0.9299 time to fit residues: 337.2863 Evaluate side-chains 232 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 136 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 995 SER Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1342 ASP Chi-restraints excluded: chain A residue 1378 GLU Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain A residue 1485 THR Chi-restraints excluded: chain A residue 1530 ASN Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1562 VAL Chi-restraints excluded: chain A residue 1606 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1702 GLU Chi-restraints excluded: chain A residue 1717 GLU Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1774 SER Chi-restraints excluded: chain A residue 1792 SER Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1860 ILE Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain A residue 1899 VAL Chi-restraints excluded: chain A residue 1927 ILE Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1948 GLU Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 2008 VAL Chi-restraints excluded: chain A residue 2013 VAL Chi-restraints excluded: chain A residue 2054 LEU Chi-restraints excluded: chain A residue 2104 VAL Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2230 TYR Chi-restraints excluded: chain A residue 2236 VAL Chi-restraints excluded: chain A residue 2273 TYR Chi-restraints excluded: chain A residue 2274 LEU Chi-restraints excluded: chain A residue 2298 ASP Chi-restraints excluded: chain A residue 2354 ASP Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 92 optimal weight: 0.5980 chunk 212 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 59 optimal weight: 8.9990 chunk 56 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 ASN ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN A1052 ASN A1058 GLN A1158 ASN A1593 ASN ** A2148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5240 r_free = 0.5240 target = 0.248489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.212348 restraints weight = 24265.662| |-----------------------------------------------------------------------------| r_work (start): 0.4909 rms_B_bonded: 3.27 r_work: 0.4503 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19471 Z= 0.177 Angle : 0.628 10.232 26343 Z= 0.331 Chirality : 0.046 0.204 2905 Planarity : 0.004 0.049 3406 Dihedral : 8.083 58.962 2638 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.03 % Favored : 92.88 % Rotamer: Outliers : 6.69 % Allowed : 34.07 % Favored : 59.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.16), residues: 2361 helix: -0.70 (0.20), residues: 645 sheet: -1.52 (0.24), residues: 421 loop : -1.66 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1743 HIS 0.003 0.001 HIS A1178 PHE 0.030 0.002 PHE A1269 TYR 0.013 0.001 TYR A 690 ARG 0.011 0.001 ARG A1281 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 152 time to evaluate : 2.427 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: A 68 ARG cc_start: 0.5754 (OUTLIER) cc_final: 0.5004 (ptp-110) REVERT: A 81 MET cc_start: 0.6315 (OUTLIER) cc_final: 0.6023 (ttt) REVERT: A 190 TYR cc_start: 0.5582 (OUTLIER) cc_final: 0.4233 (t80) REVERT: A 318 GLU cc_start: 0.4375 (OUTLIER) cc_final: 0.3841 (mp0) REVERT: A 404 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.7108 (ttpt) REVERT: A 573 ARG cc_start: 0.1670 (OUTLIER) cc_final: -0.0961 (ptt180) REVERT: A 575 LYS cc_start: 0.3093 (OUTLIER) cc_final: 0.2339 (ptpp) REVERT: A 806 ASN cc_start: 0.4975 (m-40) cc_final: 0.4733 (m-40) REVERT: A 832 ILE cc_start: 0.5123 (OUTLIER) cc_final: 0.4760 (pt) REVERT: A 974 THR cc_start: 0.3453 (OUTLIER) cc_final: 0.3145 (m) REVERT: A 1020 ASP cc_start: 0.5082 (OUTLIER) cc_final: 0.4701 (m-30) REVERT: A 1050 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7840 (tt0) REVERT: A 1058 GLN cc_start: 0.7056 (pt0) cc_final: 0.6296 (mm-40) REVERT: A 1325 LEU cc_start: 0.6490 (tp) cc_final: 0.6231 (tp) REVERT: A 1332 MET cc_start: 0.7446 (tpt) cc_final: 0.7177 (mmt) REVERT: A 1342 ASP cc_start: 0.5576 (OUTLIER) cc_final: 0.5007 (t70) REVERT: A 1421 VAL cc_start: 0.7084 (t) cc_final: 0.6865 (t) REVERT: A 1479 LYS cc_start: 0.7020 (tttm) cc_final: 0.6782 (pttp) REVERT: A 1483 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6138 (tp) REVERT: A 1613 ILE cc_start: 0.6822 (OUTLIER) cc_final: 0.6401 (tt) REVERT: A 1702 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.5444 (tp30) REVERT: A 1822 ASP cc_start: 0.5565 (m-30) cc_final: 0.5088 (m-30) REVERT: A 1854 ILE cc_start: 0.6408 (OUTLIER) cc_final: 0.6133 (mt) REVERT: A 2269 MET cc_start: -0.0105 (tpp) cc_final: -0.1174 (tpt) REVERT: A 2273 TYR cc_start: 0.3654 (OUTLIER) cc_final: 0.2794 (t80) REVERT: A 2274 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6628 (pp) REVERT: A 2298 ASP cc_start: -0.0130 (OUTLIER) cc_final: -0.0879 (p0) outliers start: 143 outliers final: 64 residues processed: 279 average time/residue: 0.9353 time to fit residues: 311.3331 Evaluate side-chains 220 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 138 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1236 TRP Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1342 ASP Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain A residue 1485 THR Chi-restraints excluded: chain A residue 1530 ASN Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1562 VAL Chi-restraints excluded: chain A residue 1606 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1641 ILE Chi-restraints excluded: chain A residue 1671 SER Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1702 GLU Chi-restraints excluded: chain A residue 1717 GLU Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1774 SER Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1860 ILE Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain A residue 1899 VAL Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1948 GLU Chi-restraints excluded: chain A residue 2008 VAL Chi-restraints excluded: chain A residue 2013 VAL Chi-restraints excluded: chain A residue 2104 VAL Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2230 TYR Chi-restraints excluded: chain A residue 2236 VAL Chi-restraints excluded: chain A residue 2273 TYR Chi-restraints excluded: chain A residue 2274 LEU Chi-restraints excluded: chain A residue 2298 ASP Chi-restraints excluded: chain A residue 2354 ASP Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 200 optimal weight: 5.9990 chunk 187 optimal weight: 0.0770 chunk 204 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 233 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 195 optimal weight: 0.1980 chunk 69 optimal weight: 3.9990 overall best weight: 1.2542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 ASN A1158 ASN A1396 ASN A1593 ASN A1727 ASN ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5206 r_free = 0.5206 target = 0.245231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.206607 restraints weight = 24287.501| |-----------------------------------------------------------------------------| r_work (start): 0.4855 rms_B_bonded: 3.39 r_work: 0.4461 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.4461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19471 Z= 0.254 Angle : 0.696 10.526 26343 Z= 0.368 Chirality : 0.048 0.213 2905 Planarity : 0.004 0.056 3406 Dihedral : 7.986 58.571 2624 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.54 % Favored : 92.38 % Rotamer: Outliers : 8.38 % Allowed : 32.94 % Favored : 58.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.16), residues: 2361 helix: -0.87 (0.19), residues: 644 sheet: -1.64 (0.24), residues: 427 loop : -1.62 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1743 HIS 0.003 0.001 HIS A1178 PHE 0.031 0.002 PHE A1269 TYR 0.028 0.002 TYR A1123 ARG 0.012 0.001 ARG A1281 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 141 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.5608 (OUTLIER) cc_final: 0.4770 (ptp-170) REVERT: A 81 MET cc_start: 0.6263 (OUTLIER) cc_final: 0.5916 (ttt) REVERT: A 170 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.6458 (mmmm) REVERT: A 190 TYR cc_start: 0.5671 (OUTLIER) cc_final: 0.4177 (t80) REVERT: A 213 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.4200 (mp0) REVERT: A 262 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.6584 (mpt180) REVERT: A 314 MET cc_start: 0.4672 (OUTLIER) cc_final: 0.3566 (mmm) REVERT: A 318 GLU cc_start: 0.4476 (OUTLIER) cc_final: 0.3830 (mp0) REVERT: A 404 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6993 (ttpt) REVERT: A 573 ARG cc_start: 0.1720 (OUTLIER) cc_final: -0.0887 (ptt180) REVERT: A 832 ILE cc_start: 0.5361 (OUTLIER) cc_final: 0.4887 (pt) REVERT: A 974 THR cc_start: 0.3784 (OUTLIER) cc_final: 0.3424 (m) REVERT: A 1019 ILE cc_start: 0.5355 (OUTLIER) cc_final: 0.4877 (tt) REVERT: A 1020 ASP cc_start: 0.4999 (OUTLIER) cc_final: 0.4511 (m-30) REVERT: A 1050 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7957 (tt0) REVERT: A 1270 ILE cc_start: 0.6131 (OUTLIER) cc_final: 0.5851 (pp) REVERT: A 1325 LEU cc_start: 0.6426 (tp) cc_final: 0.6196 (mt) REVERT: A 1332 MET cc_start: 0.7454 (tpt) cc_final: 0.7232 (mmt) REVERT: A 1342 ASP cc_start: 0.5739 (OUTLIER) cc_final: 0.5093 (t70) REVERT: A 1479 LYS cc_start: 0.6936 (tttm) cc_final: 0.6651 (pttp) REVERT: A 1483 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6355 (tp) REVERT: A 1702 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.5512 (tp30) REVERT: A 1822 ASP cc_start: 0.5957 (m-30) cc_final: 0.5637 (m-30) REVERT: A 1854 ILE cc_start: 0.6488 (OUTLIER) cc_final: 0.6194 (mt) REVERT: A 1930 LEU cc_start: 0.3137 (OUTLIER) cc_final: 0.2366 (tp) REVERT: A 1948 GLU cc_start: 0.1650 (OUTLIER) cc_final: 0.1341 (mp0) REVERT: A 1985 ILE cc_start: 0.4541 (OUTLIER) cc_final: 0.4330 (mm) REVERT: A 2269 MET cc_start: -0.0211 (tpp) cc_final: -0.1217 (tpt) REVERT: A 2274 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6693 (pp) outliers start: 179 outliers final: 96 residues processed: 296 average time/residue: 0.8932 time to fit residues: 318.5763 Evaluate side-chains 253 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 134 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLN Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 995 SER Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1236 TRP Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1334 ILE Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1342 ASP Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1394 ASP Chi-restraints excluded: chain A residue 1400 ARG Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1467 ASN Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain A residue 1530 ASN Chi-restraints excluded: chain A residue 1562 VAL Chi-restraints excluded: chain A residue 1606 ILE Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1671 SER Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1702 GLU Chi-restraints excluded: chain A residue 1717 GLU Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1774 SER Chi-restraints excluded: chain A residue 1792 SER Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1860 ILE Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain A residue 1899 VAL Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1948 GLU Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 2008 VAL Chi-restraints excluded: chain A residue 2013 VAL Chi-restraints excluded: chain A residue 2102 LEU Chi-restraints excluded: chain A residue 2104 VAL Chi-restraints excluded: chain A residue 2159 LEU Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2230 TYR Chi-restraints excluded: chain A residue 2236 VAL Chi-restraints excluded: chain A residue 2273 TYR Chi-restraints excluded: chain A residue 2274 LEU Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2312 ASN Chi-restraints excluded: chain A residue 2354 ASP Chi-restraints excluded: chain A residue 2362 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 122 optimal weight: 0.0870 chunk 100 optimal weight: 0.9990 chunk 132 optimal weight: 0.3980 chunk 54 optimal weight: 0.0980 chunk 57 optimal weight: 10.0000 chunk 229 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 HIS A 795 HIS A1052 ASN A1158 ASN ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5252 r_free = 0.5252 target = 0.249581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.211166 restraints weight = 23986.065| |-----------------------------------------------------------------------------| r_work (start): 0.4898 rms_B_bonded: 3.26 r_work: 0.4524 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6048 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19471 Z= 0.160 Angle : 0.610 9.472 26343 Z= 0.322 Chirality : 0.045 0.191 2905 Planarity : 0.004 0.060 3406 Dihedral : 7.350 57.727 2620 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.10 % Favored : 93.82 % Rotamer: Outliers : 6.36 % Allowed : 34.82 % Favored : 58.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.17), residues: 2361 helix: -0.32 (0.20), residues: 642 sheet: -1.42 (0.24), residues: 431 loop : -1.47 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1743 HIS 0.003 0.001 HIS A 185 PHE 0.032 0.001 PHE A1269 TYR 0.020 0.001 TYR A1123 ARG 0.009 0.001 ARG A2026 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 153 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.5596 (OUTLIER) cc_final: 0.4856 (ptp-110) REVERT: A 81 MET cc_start: 0.6169 (OUTLIER) cc_final: 0.5896 (ttt) REVERT: A 170 LYS cc_start: 0.6457 (OUTLIER) cc_final: 0.6125 (mmmm) REVERT: A 190 TYR cc_start: 0.5681 (OUTLIER) cc_final: 0.4063 (t80) REVERT: A 262 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6499 (mpt180) REVERT: A 314 MET cc_start: 0.4822 (OUTLIER) cc_final: 0.3772 (mmm) REVERT: A 318 GLU cc_start: 0.4216 (OUTLIER) cc_final: 0.3693 (mp0) REVERT: A 321 MET cc_start: 0.5545 (tpp) cc_final: 0.5257 (tpt) REVERT: A 404 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.7004 (ttpt) REVERT: A 445 MET cc_start: 0.5719 (tpp) cc_final: 0.5207 (tmm) REVERT: A 573 ARG cc_start: 0.1816 (OUTLIER) cc_final: -0.0647 (ptt180) REVERT: A 575 LYS cc_start: 0.3244 (OUTLIER) cc_final: 0.2391 (ptpp) REVERT: A 640 ILE cc_start: -0.0156 (OUTLIER) cc_final: -0.0991 (mp) REVERT: A 642 ASN cc_start: 0.5286 (OUTLIER) cc_final: 0.4145 (p0) REVERT: A 806 ASN cc_start: 0.5057 (m-40) cc_final: 0.4817 (m-40) REVERT: A 974 THR cc_start: 0.3285 (OUTLIER) cc_final: 0.3064 (m) REVERT: A 1020 ASP cc_start: 0.4962 (OUTLIER) cc_final: 0.4580 (m-30) REVERT: A 1050 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7983 (tt0) REVERT: A 1270 ILE cc_start: 0.6123 (OUTLIER) cc_final: 0.5872 (pp) REVERT: A 1325 LEU cc_start: 0.6373 (tp) cc_final: 0.6146 (mt) REVERT: A 1332 MET cc_start: 0.7462 (tpt) cc_final: 0.7196 (mmt) REVERT: A 1338 LEU cc_start: 0.5818 (OUTLIER) cc_final: 0.5169 (pp) REVERT: A 1342 ASP cc_start: 0.5437 (OUTLIER) cc_final: 0.4695 (t70) REVERT: A 1479 LYS cc_start: 0.6841 (tttm) cc_final: 0.6610 (pttp) REVERT: A 1483 LEU cc_start: 0.6731 (OUTLIER) cc_final: 0.6387 (tp) REVERT: A 1530 ASN cc_start: 0.7303 (OUTLIER) cc_final: 0.6951 (p0) REVERT: A 1562 VAL cc_start: 0.5858 (OUTLIER) cc_final: 0.5438 (m) REVERT: A 1822 ASP cc_start: 0.5588 (m-30) cc_final: 0.5045 (m-30) REVERT: A 1854 ILE cc_start: 0.6459 (OUTLIER) cc_final: 0.6204 (mt) REVERT: A 1948 GLU cc_start: 0.1658 (OUTLIER) cc_final: 0.1347 (mp0) REVERT: A 1959 PHE cc_start: 0.4074 (OUTLIER) cc_final: 0.3871 (m-80) REVERT: A 1985 ILE cc_start: 0.4424 (OUTLIER) cc_final: 0.4064 (pt) REVERT: A 2269 MET cc_start: -0.0270 (tpp) cc_final: -0.1254 (tpt) REVERT: A 2274 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6823 (pp) outliers start: 136 outliers final: 72 residues processed: 271 average time/residue: 0.8483 time to fit residues: 277.5199 Evaluate side-chains 238 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 141 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1145 MET Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1236 TRP Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1334 ILE Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1342 ASP Chi-restraints excluded: chain A residue 1400 ARG Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain A residue 1530 ASN Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1562 VAL Chi-restraints excluded: chain A residue 1606 ILE Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1671 SER Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1717 GLU Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1774 SER Chi-restraints excluded: chain A residue 1792 SER Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1860 ILE Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain A residue 1899 VAL Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1948 GLU Chi-restraints excluded: chain A residue 1959 PHE Chi-restraints excluded: chain A residue 1985 ILE Chi-restraints excluded: chain A residue 2008 VAL Chi-restraints excluded: chain A residue 2013 VAL Chi-restraints excluded: chain A residue 2104 VAL Chi-restraints excluded: chain A residue 2120 LEU Chi-restraints excluded: chain A residue 2159 LEU Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2230 TYR Chi-restraints excluded: chain A residue 2236 VAL Chi-restraints excluded: chain A residue 2273 TYR Chi-restraints excluded: chain A residue 2274 LEU Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2312 ASN Chi-restraints excluded: chain A residue 2354 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 89 optimal weight: 1.9990 chunk 214 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 212 optimal weight: 30.0000 chunk 213 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 174 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN A 20 GLN ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 ASN A1052 ASN A1158 ASN A1727 ASN ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5200 r_free = 0.5200 target = 0.244525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.209771 restraints weight = 24333.244| |-----------------------------------------------------------------------------| r_work (start): 0.4876 rms_B_bonded: 3.22 r_work: 0.4448 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 19471 Z= 0.286 Angle : 0.720 11.039 26343 Z= 0.380 Chirality : 0.049 0.194 2905 Planarity : 0.004 0.058 3406 Dihedral : 7.825 58.955 2615 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.96 % Favored : 91.91 % Rotamer: Outliers : 7.63 % Allowed : 34.21 % Favored : 58.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.17), residues: 2361 helix: -0.83 (0.19), residues: 642 sheet: -1.62 (0.23), residues: 447 loop : -1.56 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1743 HIS 0.003 0.001 HIS A1178 PHE 0.031 0.002 PHE A1269 TYR 0.034 0.002 TYR A1323 ARG 0.008 0.001 ARG A2026 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 151 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLN cc_start: 0.6860 (OUTLIER) cc_final: 0.6544 (mt0) REVERT: A 68 ARG cc_start: 0.5660 (OUTLIER) cc_final: 0.4655 (ptp-170) REVERT: A 81 MET cc_start: 0.6154 (OUTLIER) cc_final: 0.5822 (ttt) REVERT: A 170 LYS cc_start: 0.6644 (OUTLIER) cc_final: 0.6419 (mmmm) REVERT: A 190 TYR cc_start: 0.5690 (OUTLIER) cc_final: 0.4364 (t80) REVERT: A 191 LYS cc_start: 0.6993 (mttm) cc_final: 0.6777 (mttm) REVERT: A 213 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.4254 (mp0) REVERT: A 314 MET cc_start: 0.4561 (OUTLIER) cc_final: 0.3550 (mmm) REVERT: A 318 GLU cc_start: 0.4297 (OUTLIER) cc_final: 0.3664 (mp0) REVERT: A 404 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.7013 (ttpt) REVERT: A 573 ARG cc_start: 0.2122 (OUTLIER) cc_final: -0.0600 (ptt180) REVERT: A 640 ILE cc_start: -0.0033 (OUTLIER) cc_final: -0.0688 (mp) REVERT: A 727 MET cc_start: 0.6323 (ppp) cc_final: 0.5968 (ppp) REVERT: A 832 ILE cc_start: 0.5295 (OUTLIER) cc_final: 0.4874 (pt) REVERT: A 974 THR cc_start: 0.3766 (OUTLIER) cc_final: 0.3123 (p) REVERT: A 1019 ILE cc_start: 0.5314 (OUTLIER) cc_final: 0.4922 (tt) REVERT: A 1020 ASP cc_start: 0.5029 (OUTLIER) cc_final: 0.4514 (m-30) REVERT: A 1050 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7817 (tt0) REVERT: A 1270 ILE cc_start: 0.6222 (OUTLIER) cc_final: 0.5967 (pp) REVERT: A 1325 LEU cc_start: 0.6484 (tp) cc_final: 0.6243 (mt) REVERT: A 1332 MET cc_start: 0.7455 (tpt) cc_final: 0.7253 (mmt) REVERT: A 1479 LYS cc_start: 0.6845 (tttm) cc_final: 0.6588 (pttp) REVERT: A 1483 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6364 (tp) REVERT: A 1536 MET cc_start: 0.6327 (ppp) cc_final: 0.6106 (ptm) REVERT: A 1701 ASP cc_start: 0.5836 (OUTLIER) cc_final: 0.5282 (p0) REVERT: A 1822 ASP cc_start: 0.5985 (m-30) cc_final: 0.5685 (m-30) REVERT: A 1854 ILE cc_start: 0.6591 (OUTLIER) cc_final: 0.6312 (mt) REVERT: A 1930 LEU cc_start: 0.2966 (OUTLIER) cc_final: 0.2290 (tp) REVERT: A 1948 GLU cc_start: 0.2247 (OUTLIER) cc_final: 0.1953 (mp0) REVERT: A 2269 MET cc_start: -0.0260 (tpp) cc_final: -0.1214 (tpt) REVERT: A 2274 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6794 (pp) outliers start: 163 outliers final: 100 residues processed: 293 average time/residue: 0.8823 time to fit residues: 311.1928 Evaluate side-chains 265 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 143 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLN Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 170 LYS Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 616 GLU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 874 HIS Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1187 PHE Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1236 TRP Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1334 ILE Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1377 ILE Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1441 SER Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain A residue 1485 THR Chi-restraints excluded: chain A residue 1530 ASN Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1562 VAL Chi-restraints excluded: chain A residue 1606 ILE Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1671 SER Chi-restraints excluded: chain A residue 1685 ILE Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1701 ASP Chi-restraints excluded: chain A residue 1717 GLU Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1774 SER Chi-restraints excluded: chain A residue 1792 SER Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1860 ILE Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain A residue 1899 VAL Chi-restraints excluded: chain A residue 1930 LEU Chi-restraints excluded: chain A residue 1948 GLU Chi-restraints excluded: chain A residue 2008 VAL Chi-restraints excluded: chain A residue 2013 VAL Chi-restraints excluded: chain A residue 2102 LEU Chi-restraints excluded: chain A residue 2104 VAL Chi-restraints excluded: chain A residue 2120 LEU Chi-restraints excluded: chain A residue 2159 LEU Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2230 TYR Chi-restraints excluded: chain A residue 2236 VAL Chi-restraints excluded: chain A residue 2273 TYR Chi-restraints excluded: chain A residue 2274 LEU Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2312 ASN Chi-restraints excluded: chain A residue 2354 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 64 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 180 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 121 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 179 optimal weight: 0.5980 chunk 11 optimal weight: 0.1980 chunk 78 optimal weight: 0.3980 chunk 66 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN A 134 ASN ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN A 659 ASN A1052 ASN A1158 ASN A1593 ASN A1727 ASN ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2007 GLN ** A2148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5245 r_free = 0.5245 target = 0.249040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.209647 restraints weight = 24109.464| |-----------------------------------------------------------------------------| r_work (start): 0.4876 rms_B_bonded: 3.47 r_work: 0.4501 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19471 Z= 0.170 Angle : 0.625 10.262 26343 Z= 0.331 Chirality : 0.045 0.188 2905 Planarity : 0.004 0.065 3406 Dihedral : 7.270 58.349 2613 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.31 % Favored : 93.60 % Rotamer: Outliers : 5.38 % Allowed : 36.41 % Favored : 58.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.71 (0.17), residues: 2361 helix: -0.34 (0.20), residues: 642 sheet: -1.42 (0.24), residues: 441 loop : -1.42 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1743 HIS 0.003 0.001 HIS A1186 PHE 0.040 0.002 PHE A 335 TYR 0.030 0.001 TYR A1123 ARG 0.008 0.001 ARG A2026 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 152 time to evaluate : 2.004 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: A 68 ARG cc_start: 0.5587 (OUTLIER) cc_final: 0.4869 (ptp-110) REVERT: A 81 MET cc_start: 0.6276 (OUTLIER) cc_final: 0.6011 (ttt) REVERT: A 190 TYR cc_start: 0.5734 (OUTLIER) cc_final: 0.4255 (t80) REVERT: A 213 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.4173 (mp0) REVERT: A 262 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6529 (mpt180) REVERT: A 308 THR cc_start: 0.6761 (OUTLIER) cc_final: 0.6510 (m) REVERT: A 318 GLU cc_start: 0.4296 (OUTLIER) cc_final: 0.3661 (mp0) REVERT: A 321 MET cc_start: 0.5151 (tpp) cc_final: 0.4276 (tpt) REVERT: A 404 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.7041 (ttpt) REVERT: A 445 MET cc_start: 0.5690 (tpp) cc_final: 0.5190 (tmm) REVERT: A 531 PHE cc_start: 0.4874 (OUTLIER) cc_final: 0.4275 (t80) REVERT: A 573 ARG cc_start: 0.1841 (OUTLIER) cc_final: -0.0662 (ptt180) REVERT: A 575 LYS cc_start: 0.2992 (OUTLIER) cc_final: 0.2275 (ptpp) REVERT: A 634 TYR cc_start: 0.3300 (m-80) cc_final: 0.1957 (m-80) REVERT: A 690 TYR cc_start: 0.4435 (OUTLIER) cc_final: 0.2178 (t80) REVERT: A 727 MET cc_start: 0.6261 (ppp) cc_final: 0.5962 (ppp) REVERT: A 974 THR cc_start: 0.3397 (OUTLIER) cc_final: 0.2791 (p) REVERT: A 1020 ASP cc_start: 0.5079 (OUTLIER) cc_final: 0.4674 (m-30) REVERT: A 1050 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7868 (tt0) REVERT: A 1270 ILE cc_start: 0.6195 (OUTLIER) cc_final: 0.5959 (pp) REVERT: A 1325 LEU cc_start: 0.6405 (tp) cc_final: 0.6174 (mt) REVERT: A 1338 LEU cc_start: 0.5768 (OUTLIER) cc_final: 0.4891 (pp) REVERT: A 1479 LYS cc_start: 0.6844 (tttm) cc_final: 0.6573 (pttp) REVERT: A 1483 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6691 (tp) REVERT: A 1530 ASN cc_start: 0.7299 (OUTLIER) cc_final: 0.6996 (p0) REVERT: A 1536 MET cc_start: 0.6176 (ppp) cc_final: 0.5926 (ptm) REVERT: A 1822 ASP cc_start: 0.5611 (m-30) cc_final: 0.5027 (m-30) REVERT: A 1854 ILE cc_start: 0.6501 (OUTLIER) cc_final: 0.6266 (mt) REVERT: A 1948 GLU cc_start: 0.1648 (OUTLIER) cc_final: 0.1394 (mp0) REVERT: A 2249 MET cc_start: 0.3593 (mmp) cc_final: 0.3313 (tpp) REVERT: A 2269 MET cc_start: -0.0281 (tpp) cc_final: -0.1234 (tpt) REVERT: A 2274 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6881 (pp) REVERT: A 2312 ASN cc_start: 0.4335 (OUTLIER) cc_final: 0.4027 (p0) outliers start: 115 outliers final: 75 residues processed: 257 average time/residue: 0.9060 time to fit residues: 280.7507 Evaluate side-chains 234 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 137 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1187 PHE Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1236 TRP Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1334 ILE Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain A residue 1530 ASN Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1562 VAL Chi-restraints excluded: chain A residue 1606 ILE Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1671 SER Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1717 GLU Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1792 SER Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1860 ILE Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain A residue 1899 VAL Chi-restraints excluded: chain A residue 1948 GLU Chi-restraints excluded: chain A residue 2008 VAL Chi-restraints excluded: chain A residue 2013 VAL Chi-restraints excluded: chain A residue 2104 VAL Chi-restraints excluded: chain A residue 2120 LEU Chi-restraints excluded: chain A residue 2159 LEU Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2230 TYR Chi-restraints excluded: chain A residue 2236 VAL Chi-restraints excluded: chain A residue 2273 TYR Chi-restraints excluded: chain A residue 2274 LEU Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2312 ASN Chi-restraints excluded: chain A residue 2354 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 0.0070 chunk 20 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 7 optimal weight: 0.5980 chunk 209 optimal weight: 20.0000 chunk 83 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 ASN A1158 ASN A1396 ASN A1663 HIS ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5230 r_free = 0.5230 target = 0.248130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.208429 restraints weight = 24022.314| |-----------------------------------------------------------------------------| r_work (start): 0.4868 rms_B_bonded: 3.59 r_work: 0.4490 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19471 Z= 0.189 Angle : 0.641 10.096 26343 Z= 0.338 Chirality : 0.046 0.205 2905 Planarity : 0.004 0.064 3406 Dihedral : 7.193 59.652 2612 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.61 % Favored : 93.31 % Rotamer: Outliers : 5.33 % Allowed : 36.31 % Favored : 58.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.67 (0.17), residues: 2361 helix: -0.29 (0.20), residues: 639 sheet: -1.40 (0.24), residues: 441 loop : -1.40 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1743 HIS 0.003 0.001 HIS A1186 PHE 0.035 0.002 PHE A2031 TYR 0.026 0.001 TYR A1123 ARG 0.013 0.001 ARG A1309 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 149 time to evaluate : 2.008 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: A 68 ARG cc_start: 0.5612 (OUTLIER) cc_final: 0.4513 (ptp-170) REVERT: A 81 MET cc_start: 0.6344 (OUTLIER) cc_final: 0.6012 (ttt) REVERT: A 190 TYR cc_start: 0.5615 (OUTLIER) cc_final: 0.4173 (t80) REVERT: A 213 GLU cc_start: 0.6558 (OUTLIER) cc_final: 0.4329 (mp0) REVERT: A 262 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6567 (mpt180) REVERT: A 318 GLU cc_start: 0.4255 (OUTLIER) cc_final: 0.3643 (mp0) REVERT: A 404 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.7045 (ttpt) REVERT: A 445 MET cc_start: 0.5734 (tpp) cc_final: 0.5337 (tmm) REVERT: A 573 ARG cc_start: 0.1890 (OUTLIER) cc_final: -0.0613 (ptt180) REVERT: A 575 LYS cc_start: 0.2908 (OUTLIER) cc_final: 0.2142 (ptpp) REVERT: A 640 ILE cc_start: -0.0089 (OUTLIER) cc_final: -0.0849 (mp) REVERT: A 690 TYR cc_start: 0.4546 (OUTLIER) cc_final: 0.2144 (t80) REVERT: A 727 MET cc_start: 0.6266 (ppp) cc_final: 0.5962 (ppp) REVERT: A 920 GLU cc_start: 0.6276 (tp30) cc_final: 0.6006 (tm-30) REVERT: A 974 THR cc_start: 0.3369 (OUTLIER) cc_final: 0.2771 (p) REVERT: A 1020 ASP cc_start: 0.5098 (OUTLIER) cc_final: 0.4671 (m-30) REVERT: A 1050 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7933 (tt0) REVERT: A 1270 ILE cc_start: 0.6214 (OUTLIER) cc_final: 0.5974 (pp) REVERT: A 1325 LEU cc_start: 0.6366 (tp) cc_final: 0.6135 (mt) REVERT: A 1338 LEU cc_start: 0.5736 (OUTLIER) cc_final: 0.5011 (pp) REVERT: A 1479 LYS cc_start: 0.6833 (tttm) cc_final: 0.6570 (pttp) REVERT: A 1483 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6812 (tp) REVERT: A 1530 ASN cc_start: 0.7205 (OUTLIER) cc_final: 0.6916 (p0) REVERT: A 1536 MET cc_start: 0.6205 (ppp) cc_final: 0.5954 (ptm) REVERT: A 1822 ASP cc_start: 0.5971 (m-30) cc_final: 0.5420 (m-30) REVERT: A 1854 ILE cc_start: 0.6528 (OUTLIER) cc_final: 0.6271 (mt) REVERT: A 2269 MET cc_start: -0.0286 (tpp) cc_final: -0.1241 (tpt) REVERT: A 2274 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6762 (pp) REVERT: A 2312 ASN cc_start: 0.4548 (OUTLIER) cc_final: 0.4237 (p0) outliers start: 114 outliers final: 76 residues processed: 256 average time/residue: 0.9377 time to fit residues: 290.9041 Evaluate side-chains 238 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 142 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLN Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 642 ASN Chi-restraints excluded: chain A residue 660 THR Chi-restraints excluded: chain A residue 690 TYR Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 849 SER Chi-restraints excluded: chain A residue 855 ILE Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1020 ASP Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1167 CYS Chi-restraints excluded: chain A residue 1187 PHE Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1236 TRP Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1334 ILE Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1383 ILE Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1418 ILE Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain A residue 1530 ASN Chi-restraints excluded: chain A residue 1549 THR Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1562 VAL Chi-restraints excluded: chain A residue 1606 ILE Chi-restraints excluded: chain A residue 1671 SER Chi-restraints excluded: chain A residue 1698 LEU Chi-restraints excluded: chain A residue 1717 GLU Chi-restraints excluded: chain A residue 1748 SER Chi-restraints excluded: chain A residue 1792 SER Chi-restraints excluded: chain A residue 1833 VAL Chi-restraints excluded: chain A residue 1854 ILE Chi-restraints excluded: chain A residue 1858 THR Chi-restraints excluded: chain A residue 1860 ILE Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain A residue 1899 VAL Chi-restraints excluded: chain A residue 1967 LEU Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 2008 VAL Chi-restraints excluded: chain A residue 2013 VAL Chi-restraints excluded: chain A residue 2104 VAL Chi-restraints excluded: chain A residue 2120 LEU Chi-restraints excluded: chain A residue 2159 LEU Chi-restraints excluded: chain A residue 2165 THR Chi-restraints excluded: chain A residue 2230 TYR Chi-restraints excluded: chain A residue 2236 VAL Chi-restraints excluded: chain A residue 2273 TYR Chi-restraints excluded: chain A residue 2274 LEU Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2312 ASN Chi-restraints excluded: chain A residue 2354 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 137 optimal weight: 0.4980 chunk 217 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 224 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 ASN A1158 ASN A1727 ASN ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5232 r_free = 0.5232 target = 0.247652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.209311 restraints weight = 24129.623| |-----------------------------------------------------------------------------| r_work (start): 0.4873 rms_B_bonded: 3.46 r_work: 0.4479 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19471 Z= 0.201 Angle : 0.650 10.530 26343 Z= 0.344 Chirality : 0.047 0.195 2905 Planarity : 0.004 0.069 3406 Dihedral : 7.156 59.814 2606 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.07 % Favored : 92.84 % Rotamer: Outliers : 5.24 % Allowed : 36.50 % Favored : 58.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.69 (0.17), residues: 2361 helix: -0.35 (0.20), residues: 637 sheet: -1.38 (0.24), residues: 445 loop : -1.40 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1743 HIS 0.002 0.001 HIS A1178 PHE 0.042 0.002 PHE A 335 TYR 0.020 0.001 TYR A1323 ARG 0.008 0.001 ARG A2026 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15297.46 seconds wall clock time: 270 minutes 25.00 seconds (16225.00 seconds total)