Starting phenix.real_space_refine on Sun Oct 12 00:35:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2h_38010/10_2025/8x2h_38010.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2h_38010/10_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_38010/10_2025/8x2h_38010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2h_38010/10_2025/8x2h_38010.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2h_38010/10_2025/8x2h_38010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2h_38010/10_2025/8x2h_38010.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 4.07, per 1000 atoms: 0.21 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: 1.43 Conformation dependent library (CDL) restraints added in 705.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.02 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: 5.98 Time building geometry restraints manager: 1.98 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: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 22.000 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.850 ------------------------------------------------------------------------------- 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 : 0.006 0.487 19473 Z= 0.262 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 : 16.35 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG A1241 TYR 0.026 0.002 TYR A1531 PHE 0.034 0.002 PHE A 539 TRP 0.019 0.002 TRP A1743 HIS 0.007 0.001 HIS A1178 Details of bonding type rmsd covalent geometry : bond 0.00457 (19471) covalent geometry : angle 0.84647 (26343) hydrogen bonds : bond 0.13299 ( 714) hydrogen bonds : angle 7.58798 ( 1914) metal coordination : bond 0.40851 ( 2) *********************** 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 : 0.600 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: 0.4291 time to fit residues: 238.1490 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 : 0.756 ------------------------------------------------------------------------------- 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 216 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN A 343 GLN A 379 ASN A 479 GLN A 510 GLN A 579 HIS ** A 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 ASN A 846 ASN A 853 ASN ** A1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 GLN A1257 HIS A1294 ASN ** A1307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1370 ASN A1453 ASN A1456 HIS A1504 ASN A1520 ASN A1530 ASN ** A1593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1727 ASN A1735 ASN A1763 GLN A1840 ASN ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1925 ASN A2002 ASN A2058 ASN A2176 ASN A2196 ASN A2234 ASN A2312 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5176 r_free = 0.5176 target = 0.243644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.206806 restraints weight = 24695.325| |-----------------------------------------------------------------------------| r_work (start): 0.4826 rms_B_bonded: 1.77 r_work: 0.4549 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.4458 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.4458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19473 Z= 0.219 Angle : 0.803 11.433 26343 Z= 0.425 Chirality : 0.051 0.208 2905 Planarity : 0.005 0.069 3406 Dihedral : 12.436 73.705 2832 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.36 % Favored : 90.51 % Rotamer: Outliers : 11.89 % Allowed : 29.95 % Favored : 58.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.56 (0.15), residues: 2361 helix: -2.42 (0.17), residues: 635 sheet: -2.30 (0.24), residues: 413 loop : -2.37 (0.15), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 273 TYR 0.028 0.002 TYR A1531 PHE 0.035 0.003 PHE A 539 TRP 0.017 0.002 TRP A1743 HIS 0.005 0.001 HIS A1663 Details of bonding type rmsd covalent geometry : bond 0.00498 (19471) covalent geometry : angle 0.80344 (26343) hydrogen bonds : bond 0.05547 ( 714) hydrogen bonds : angle 6.57536 ( 1914) metal coordination : bond 0.01141 ( 2) *********************** 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 419 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 254 poor density : 165 time to evaluate : 0.753 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 8 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7361 (mt0) REVERT: A 68 ARG cc_start: 0.5928 (OUTLIER) cc_final: 0.5105 (ptp-170) REVERT: A 141 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.6199 (tp) REVERT: A 161 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6935 (tp) REVERT: A 190 TYR cc_start: 0.5125 (OUTLIER) cc_final: 0.4126 (t80) REVERT: A 262 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6957 (mmt90) REVERT: A 318 GLU cc_start: 0.4825 (OUTLIER) cc_final: 0.4617 (mp0) REVERT: A 404 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.7150 (ttpt) REVERT: A 447 MET cc_start: 0.7000 (mtm) cc_final: 0.6699 (mtm) REVERT: A 454 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7332 (mt) REVERT: A 530 GLN cc_start: 0.5854 (OUTLIER) cc_final: 0.5318 (tp40) REVERT: A 573 ARG cc_start: 0.1622 (OUTLIER) cc_final: -0.0006 (ptt180) REVERT: A 642 ASN cc_start: 0.5020 (OUTLIER) cc_final: 0.4669 (p0) REVERT: A 690 TYR cc_start: 0.4622 (OUTLIER) cc_final: 0.2521 (t80) REVERT: A 832 ILE cc_start: 0.5484 (OUTLIER) cc_final: 0.5119 (pt) REVERT: A 974 THR cc_start: 0.3985 (OUTLIER) cc_final: 0.3309 (p) REVERT: A 1058 GLN cc_start: 0.7184 (pt0) cc_final: 0.6388 (mm-40) REVERT: A 1092 LEU cc_start: 0.1049 (OUTLIER) cc_final: 0.0691 (tp) REVERT: A 1145 MET cc_start: 0.5642 (ttp) cc_final: 0.5416 (ttp) REVERT: A 1270 ILE cc_start: 0.6340 (OUTLIER) cc_final: 0.6024 (pp) REVERT: A 1281 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6079 (pmt-80) REVERT: A 1314 TYR cc_start: 0.4956 (OUTLIER) cc_final: 0.3180 (m-80) REVERT: A 1342 ASP cc_start: 0.5742 (OUTLIER) cc_final: 0.5103 (t70) REVERT: A 1472 ASN cc_start: 0.6581 (OUTLIER) cc_final: 0.6222 (m-40) REVERT: A 1663 HIS cc_start: 0.5878 (OUTLIER) cc_final: 0.3782 (p-80) REVERT: A 1703 ILE cc_start: 0.6068 (OUTLIER) cc_final: 0.5742 (mt) REVERT: A 1715 CYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6764 (t) REVERT: A 1752 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5939 (mp) REVERT: A 1810 PHE cc_start: 0.4629 (OUTLIER) cc_final: 0.4425 (p90) REVERT: A 1854 ILE cc_start: 0.6404 (OUTLIER) cc_final: 0.6075 (mt) REVERT: A 1959 PHE cc_start: 0.4787 (OUTLIER) cc_final: 0.4581 (m-80) REVERT: A 1985 ILE cc_start: 0.4270 (OUTLIER) cc_final: 0.3897 (mm) REVERT: A 1988 THR cc_start: 0.4260 (OUTLIER) cc_final: 0.3977 (t) REVERT: A 2265 GLU cc_start: 0.1300 (OUTLIER) cc_final: 0.1087 (tp30) REVERT: A 2298 ASP cc_start: -0.0432 (OUTLIER) cc_final: -0.0665 (p0) REVERT: A 2329 LYS cc_start: 0.3117 (OUTLIER) cc_final: 0.2630 (tptp) outliers start: 254 outliers final: 112 residues processed: 388 average time/residue: 0.4596 time to fit residues: 210.0918 Evaluate side-chains 289 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 144 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 48 LYS Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 92 THR 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 141 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 146 VAL 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 201 ILE 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 262 ARG 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 351 SER Chi-restraints excluded: chain A residue 359 ILE 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 409 ILE 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 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 530 GLN 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 700 MET 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 767 SER 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 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 875 GLN 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 1034 THR 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 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 1205 VAL Chi-restraints excluded: chain A residue 1221 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 1314 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 1405 THR 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 1606 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1618 SER Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1641 ILE 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 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 1752 LEU Chi-restraints excluded: chain A residue 1774 SER Chi-restraints excluded: chain A residue 1790 ASP Chi-restraints excluded: chain A residue 1792 SER Chi-restraints excluded: chain A residue 1810 PHE Chi-restraints excluded: chain A residue 1837 ILE Chi-restraints excluded: chain A residue 1843 LEU 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 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 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 2006 MET 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 2230 TYR 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 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 32 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 212 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 150 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 583 GLN ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 HIS ** A1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** A1892 GLN ** A1960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2260 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5190 r_free = 0.5190 target = 0.243565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.207473 restraints weight = 24498.407| |-----------------------------------------------------------------------------| r_work (start): 0.4864 rms_B_bonded: 3.29 r_work: 0.4468 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19473 Z= 0.197 Angle : 0.755 12.243 26343 Z= 0.400 Chirality : 0.050 0.180 2905 Planarity : 0.005 0.065 3406 Dihedral : 10.854 67.588 2732 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.09 % Favored : 91.78 % Rotamer: Outliers : 10.90 % Allowed : 30.88 % Favored : 58.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.15 (0.15), residues: 2361 helix: -1.96 (0.18), residues: 640 sheet: -2.15 (0.24), residues: 413 loop : -2.14 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1309 TYR 0.021 0.002 TYR A1531 PHE 0.034 0.002 PHE A 539 TRP 0.017 0.001 TRP A1743 HIS 0.004 0.001 HIS A1178 Details of bonding type rmsd covalent geometry : bond 0.00450 (19471) covalent geometry : angle 0.75488 (26343) hydrogen bonds : bond 0.05056 ( 714) hydrogen bonds : angle 6.27669 ( 1914) metal coordination : bond 0.00310 ( 2) *********************** 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 382 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 149 time to evaluate : 0.530 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: 0.5739 (OUTLIER) cc_final: 0.4793 (ptp-170) REVERT: A 81 MET cc_start: 0.6159 (OUTLIER) cc_final: 0.5546 (tpt) REVERT: A 190 TYR cc_start: 0.5505 (OUTLIER) cc_final: 0.4111 (t80) REVERT: A 318 GLU cc_start: 0.4964 (OUTLIER) cc_final: 0.4361 (mp0) REVERT: A 333 LYS cc_start: 0.6321 (OUTLIER) cc_final: 0.6067 (pttp) REVERT: A 404 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7201 (ttpt) REVERT: A 415 ASN cc_start: 0.6982 (OUTLIER) cc_final: 0.6737 (t0) REVERT: A 454 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7424 (mt) REVERT: A 530 GLN cc_start: 0.5735 (OUTLIER) cc_final: 0.5164 (tp40) REVERT: A 573 ARG cc_start: 0.1841 (OUTLIER) cc_final: 0.0313 (ptt180) REVERT: A 599 SER cc_start: 0.4821 (OUTLIER) cc_final: 0.4598 (t) REVERT: A 642 ASN cc_start: 0.5407 (OUTLIER) cc_final: 0.4966 (p0) REVERT: A 741 GLN cc_start: 0.6112 (OUTLIER) cc_final: 0.5629 (pp30) REVERT: A 780 PHE cc_start: 0.4543 (OUTLIER) cc_final: 0.3750 (t80) REVERT: A 832 ILE cc_start: 0.5434 (OUTLIER) cc_final: 0.5021 (pt) REVERT: A 965 ILE cc_start: 0.6264 (OUTLIER) cc_final: 0.6038 (mp) REVERT: A 974 THR cc_start: 0.3668 (OUTLIER) cc_final: 0.3255 (m) REVERT: A 1020 ASP cc_start: 0.4912 (OUTLIER) cc_final: 0.4467 (m-30) REVERT: A 1050 GLU cc_start: 0.8276 (tm-30) cc_final: 0.8048 (tt0) REVERT: A 1058 GLN cc_start: 0.7270 (pt0) cc_final: 0.6430 (mm-40) REVERT: A 1092 LEU cc_start: 0.1320 (OUTLIER) cc_final: 0.1028 (tp) REVERT: A 1164 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6210 (pp) REVERT: A 1270 ILE cc_start: 0.6326 (OUTLIER) cc_final: 0.5951 (pp) REVERT: A 1281 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.7058 (pmm-80) REVERT: A 1305 THR cc_start: 0.4051 (OUTLIER) cc_final: 0.3840 (p) REVERT: A 1342 ASP cc_start: 0.5679 (OUTLIER) cc_final: 0.5057 (t70) REVERT: A 1355 ILE cc_start: 0.5553 (mm) cc_final: 0.5081 (mm) REVERT: A 1364 LYS cc_start: 0.3178 (OUTLIER) cc_final: 0.2170 (mttt) REVERT: A 1472 ASN cc_start: 0.6722 (OUTLIER) cc_final: 0.6303 (m-40) REVERT: A 1474 PHE cc_start: 0.6975 (m-80) cc_final: 0.6689 (t80) REVERT: A 1479 LYS cc_start: 0.7069 (tttm) cc_final: 0.6816 (pttp) REVERT: A 1703 ILE cc_start: 0.5985 (OUTLIER) cc_final: 0.5721 (mt) REVERT: A 1854 ILE cc_start: 0.6408 (OUTLIER) cc_final: 0.6089 (mt) REVERT: A 1930 LEU cc_start: 0.3225 (OUTLIER) cc_final: 0.2453 (tp) REVERT: A 1959 PHE cc_start: 0.4855 (OUTLIER) cc_final: 0.4562 (m-80) REVERT: A 1985 ILE cc_start: 0.3973 (OUTLIER) cc_final: 0.3743 (mm) REVERT: A 2216 GLU cc_start: 0.3856 (OUTLIER) cc_final: 0.3434 (tm-30) REVERT: A 2273 TYR cc_start: 0.3684 (OUTLIER) cc_final: 0.3436 (m-80) outliers start: 233 outliers final: 110 residues processed: 362 average time/residue: 0.4226 time to fit residues: 181.6973 Evaluate side-chains 280 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 137 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 87 LYS 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 145 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 194 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 260 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 368 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 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 530 GLN Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 573 ARG Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain A residue 616 GLU 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 704 SER Chi-restraints excluded: chain A residue 731 SER Chi-restraints excluded: chain A residue 741 GLN 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 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 862 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 948 VAL Chi-restraints excluded: chain A residue 965 ILE 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 1045 ILE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1118 THR 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 1222 LEU Chi-restraints excluded: chain A residue 1248 THR 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 1305 THR 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 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 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 1618 SER Chi-restraints excluded: chain A residue 1623 GLU Chi-restraints excluded: chain A residue 1624 LEU Chi-restraints excluded: chain A residue 1644 THR Chi-restraints excluded: chain A residue 1645 SER Chi-restraints excluded: chain A residue 1685 ILE 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 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 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 1860 ILE 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 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 2006 MET Chi-restraints excluded: chain A residue 2008 VAL 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 2216 GLU 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 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 10 optimal weight: 0.0770 chunk 153 optimal weight: 0.0040 chunk 9 optimal weight: 0.7980 chunk 205 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 193 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 overall best weight: 0.4950 ------------------------------------------------------------------------------- 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 405 ASN A 553 GLN ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1396 ASN A1593 ASN A1631 ASN ** A2148 ASN ** 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 = 0.5239 r_free = 0.5239 target = 0.248998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.212481 restraints weight = 24199.216| |-----------------------------------------------------------------------------| r_work (start): 0.4904 rms_B_bonded: 3.30 r_work: 0.4501 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19473 Z= 0.119 Angle : 0.632 10.339 26343 Z= 0.332 Chirality : 0.046 0.199 2905 Planarity : 0.004 0.048 3406 Dihedral : 8.961 61.004 2684 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.52 % Favored : 93.39 % Rotamer: Outliers : 7.39 % Allowed : 33.08 % Favored : 59.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.16), residues: 2361 helix: -1.03 (0.19), residues: 644 sheet: -1.77 (0.24), residues: 420 loop : -1.84 (0.16), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1400 TYR 0.015 0.001 TYR A 125 PHE 0.028 0.001 PHE A1269 TRP 0.013 0.001 TRP A1743 HIS 0.003 0.001 HIS A1178 Details of bonding type rmsd covalent geometry : bond 0.00259 (19471) covalent geometry : angle 0.63160 (26343) hydrogen bonds : bond 0.03650 ( 714) hydrogen bonds : angle 5.51351 ( 1914) metal coordination : bond 0.00068 ( 2) *********************** 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 318 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 160 time to evaluate : 0.644 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: 0.5625 (OUTLIER) cc_final: 0.4832 (ptp-170) REVERT: A 81 MET cc_start: 0.6249 (OUTLIER) cc_final: 0.5976 (ttt) REVERT: A 159 GLU cc_start: 0.5578 (OUTLIER) cc_final: 0.4974 (pm20) REVERT: A 190 TYR cc_start: 0.5493 (OUTLIER) cc_final: 0.3740 (t80) REVERT: A 318 GLU cc_start: 0.5041 (OUTLIER) cc_final: 0.4445 (mp0) REVERT: A 402 GLN cc_start: 0.6363 (OUTLIER) cc_final: 0.6031 (tp40) REVERT: A 530 GLN cc_start: 0.5920 (OUTLIER) cc_final: 0.5670 (mm-40) REVERT: A 573 ARG cc_start: 0.1743 (OUTLIER) cc_final: -0.1367 (ptm160) REVERT: A 575 LYS cc_start: 0.3310 (OUTLIER) cc_final: 0.2482 (ptpp) REVERT: A 642 ASN cc_start: 0.5179 (OUTLIER) cc_final: 0.4314 (p0) REVERT: A 832 ILE cc_start: 0.5172 (OUTLIER) cc_final: 0.4774 (pt) REVERT: A 1020 ASP cc_start: 0.4756 (OUTLIER) cc_final: 0.4405 (m-30) REVERT: A 1050 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7943 (tt0) REVERT: A 1058 GLN cc_start: 0.6943 (pt0) cc_final: 0.6096 (mm-40) REVERT: A 1092 LEU cc_start: 0.1718 (OUTLIER) cc_final: 0.1507 (tt) REVERT: A 1270 ILE cc_start: 0.6162 (OUTLIER) cc_final: 0.5916 (pp) REVERT: A 1310 LYS cc_start: 0.7414 (mtmm) cc_final: 0.7170 (pmtt) REVERT: A 1342 ASP cc_start: 0.5694 (OUTLIER) cc_final: 0.5136 (t70) REVERT: A 1405 THR cc_start: 0.7046 (OUTLIER) cc_final: 0.6829 (p) REVERT: A 1472 ASN cc_start: 0.6405 (OUTLIER) cc_final: 0.5896 (m-40) REVERT: A 1474 PHE cc_start: 0.7030 (m-80) cc_final: 0.6804 (t80) REVERT: A 1483 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6233 (tp) REVERT: A 1613 ILE cc_start: 0.6774 (OUTLIER) cc_final: 0.6446 (tt) REVERT: A 1959 PHE cc_start: 0.4762 (OUTLIER) cc_final: 0.4467 (m-80) REVERT: A 2273 TYR cc_start: 0.4132 (OUTLIER) cc_final: 0.3486 (t80) REVERT: A 2274 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6636 (pt) REVERT: A 2298 ASP cc_start: 0.0136 (OUTLIER) cc_final: -0.0220 (p0) REVERT: A 2309 LEU cc_start: 0.4634 (OUTLIER) cc_final: 0.4370 (tm) outliers start: 158 outliers final: 69 residues processed: 301 average time/residue: 0.4509 time to fit residues: 159.5519 Evaluate side-chains 233 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 140 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 159 GLU Chi-restraints excluded: chain A residue 190 TYR 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 318 GLU Chi-restraints excluded: chain A residue 336 ASP 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 417 SER Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 530 GLN 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 731 SER Chi-restraints excluded: chain A residue 762 ILE 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 855 ILE 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 1092 LEU 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 1221 VAL Chi-restraints excluded: chain A residue 1248 THR Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1339 VAL 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 1405 THR Chi-restraints excluded: chain A residue 1418 ILE 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 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 1698 LEU 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 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 1970 LEU 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 2127 ASP 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 2273 TYR Chi-restraints excluded: chain A residue 2274 LEU Chi-restraints excluded: chain A residue 2298 ASP Chi-restraints excluded: chain A residue 2309 LEU 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 193 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 234 optimal weight: 30.0000 chunk 40 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 184 optimal weight: 0.6980 chunk 120 optimal weight: 0.5980 chunk 113 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN A 88 ASN A 152 ASN ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS ** A1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 ASN ** A1307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2148 ASN ** 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 = 0.5242 r_free = 0.5242 target = 0.248559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.209430 restraints weight = 24337.405| |-----------------------------------------------------------------------------| r_work (start): 0.4876 rms_B_bonded: 3.46 r_work: 0.4503 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19473 Z= 0.123 Angle : 0.620 9.880 26343 Z= 0.328 Chirality : 0.046 0.184 2905 Planarity : 0.004 0.048 3406 Dihedral : 8.138 58.687 2639 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.69 % Favored : 93.22 % Rotamer: Outliers : 7.21 % Allowed : 33.69 % Favored : 59.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.16), residues: 2361 helix: -0.65 (0.20), residues: 643 sheet: -1.53 (0.24), residues: 420 loop : -1.63 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1495 TYR 0.014 0.001 TYR A1477 PHE 0.030 0.001 PHE A1269 TRP 0.011 0.001 TRP A1743 HIS 0.003 0.001 HIS A1178 Details of bonding type rmsd covalent geometry : bond 0.00273 (19471) covalent geometry : angle 0.62012 (26343) hydrogen bonds : bond 0.03619 ( 714) hydrogen bonds : angle 5.35671 ( 1914) metal coordination : bond 0.00029 ( 2) *********************** 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 308 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 154 time to evaluate : 0.699 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 18 ARG cc_start: 0.6504 (OUTLIER) cc_final: 0.5974 (mtt-85) REVERT: A 68 ARG cc_start: 0.5735 (OUTLIER) cc_final: 0.4984 (ptp-110) REVERT: A 81 MET cc_start: 0.6278 (OUTLIER) cc_final: 0.5963 (ttt) REVERT: A 190 TYR cc_start: 0.5496 (OUTLIER) cc_final: 0.3797 (t80) REVERT: A 318 GLU cc_start: 0.4779 (OUTLIER) cc_final: 0.4135 (mp0) REVERT: A 395 CYS cc_start: 0.5542 (OUTLIER) cc_final: 0.5276 (m) REVERT: A 402 GLN cc_start: 0.6375 (OUTLIER) cc_final: 0.6056 (tp40) REVERT: A 404 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7070 (ttpt) REVERT: A 445 MET cc_start: 0.5864 (tpp) cc_final: 0.5379 (tmm) REVERT: A 530 GLN cc_start: 0.5967 (OUTLIER) cc_final: 0.5684 (mm-40) REVERT: A 573 ARG cc_start: 0.1537 (OUTLIER) cc_final: -0.1003 (ptt180) REVERT: A 575 LYS cc_start: 0.2890 (OUTLIER) cc_final: 0.2110 (ptpp) REVERT: A 642 ASN cc_start: 0.5306 (OUTLIER) cc_final: 0.4328 (p0) REVERT: A 806 ASN cc_start: 0.5232 (m-40) cc_final: 0.5026 (m-40) REVERT: A 974 THR cc_start: 0.3357 (OUTLIER) cc_final: 0.3125 (m) REVERT: A 1020 ASP cc_start: 0.4979 (OUTLIER) cc_final: 0.4609 (m-30) REVERT: A 1050 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8029 (tt0) REVERT: A 1058 GLN cc_start: 0.6938 (pt0) cc_final: 0.6049 (mm-40) REVERT: A 1155 ILE cc_start: 0.4112 (OUTLIER) cc_final: 0.3903 (mp) REVERT: A 1270 ILE cc_start: 0.5981 (OUTLIER) cc_final: 0.5768 (pp) REVERT: A 1325 LEU cc_start: 0.6412 (tp) cc_final: 0.6166 (mt) REVERT: A 1472 ASN cc_start: 0.6397 (OUTLIER) cc_final: 0.5795 (m-40) REVERT: A 1483 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6340 (tp) REVERT: A 1613 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6426 (mm) REVERT: A 1702 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.5335 (tp30) REVERT: A 1798 SER cc_start: 0.6587 (OUTLIER) cc_final: 0.6236 (p) REVERT: A 1930 LEU cc_start: 0.3295 (OUTLIER) cc_final: 0.2552 (tp) REVERT: A 1959 PHE cc_start: 0.4465 (OUTLIER) cc_final: 0.4213 (m-80) REVERT: A 2269 MET cc_start: -0.0216 (tpp) cc_final: -0.1144 (tpt) REVERT: A 2273 TYR cc_start: 0.3996 (OUTLIER) cc_final: 0.3406 (t80) REVERT: A 2274 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6752 (pp) REVERT: A 2298 ASP cc_start: 0.0502 (OUTLIER) cc_final: -0.0744 (p0) outliers start: 154 outliers final: 74 residues processed: 293 average time/residue: 0.4479 time to fit residues: 155.3428 Evaluate side-chains 239 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 139 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG 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 190 TYR 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 260 VAL Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 365 ASP 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 417 SER Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 572 THR 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 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 836 ILE Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 855 ILE 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 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 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 1334 ILE Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1378 GLU Chi-restraints excluded: chain A residue 1383 ILE 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 1441 SER 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 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 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 1798 SER 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 1959 PHE 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 2127 ASP Chi-restraints excluded: chain A residue 2159 LEU 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 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 148 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 10 optimal weight: 0.0070 chunk 213 optimal weight: 0.0370 chunk 127 optimal weight: 1.9990 chunk 228 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.1880 ------------------------------------------------------------------------------- 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 197 ASN ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 ASN A1396 ASN A1727 ASN ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2148 ASN ** 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 = 0.5211 r_free = 0.5211 target = 0.245609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.206805 restraints weight = 24168.907| |-----------------------------------------------------------------------------| r_work (start): 0.4852 rms_B_bonded: 3.71 r_work: 0.4445 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19473 Z= 0.162 Angle : 0.671 9.614 26343 Z= 0.357 Chirality : 0.048 0.177 2905 Planarity : 0.004 0.058 3406 Dihedral : 8.220 58.543 2633 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.67 % Favored : 92.25 % Rotamer: Outliers : 8.47 % Allowed : 32.62 % Favored : 58.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.17), residues: 2361 helix: -0.82 (0.19), residues: 649 sheet: -1.39 (0.25), residues: 423 loop : -1.65 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1400 TYR 0.018 0.002 TYR A1531 PHE 0.033 0.002 PHE A 531 TRP 0.011 0.001 TRP A1743 HIS 0.003 0.001 HIS A1178 Details of bonding type rmsd covalent geometry : bond 0.00369 (19471) covalent geometry : angle 0.67080 (26343) hydrogen bonds : bond 0.04166 ( 714) hydrogen bonds : angle 5.58313 ( 1914) metal coordination : bond 0.00149 ( 2) *********************** 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 328 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 147 time to evaluate : 0.698 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 14 TYR cc_start: 0.5560 (OUTLIER) cc_final: 0.5250 (p90) REVERT: A 18 ARG cc_start: 0.6710 (OUTLIER) cc_final: 0.6045 (mtt-85) REVERT: A 68 ARG cc_start: 0.5669 (OUTLIER) cc_final: 0.4721 (ptp-170) REVERT: A 81 MET cc_start: 0.6249 (OUTLIER) cc_final: 0.5918 (ttt) REVERT: A 190 TYR cc_start: 0.5714 (OUTLIER) cc_final: 0.4448 (t80) REVERT: A 191 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6710 (mttm) REVERT: A 213 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.4190 (mp0) REVERT: A 314 MET cc_start: 0.4509 (OUTLIER) cc_final: 0.3396 (mmm) REVERT: A 318 GLU cc_start: 0.5004 (OUTLIER) cc_final: 0.4187 (mp0) REVERT: A 395 CYS cc_start: 0.5558 (OUTLIER) cc_final: 0.5346 (m) REVERT: A 530 GLN cc_start: 0.5918 (OUTLIER) cc_final: 0.5455 (tp40) REVERT: A 573 ARG cc_start: 0.2019 (OUTLIER) cc_final: -0.0737 (ptt180) REVERT: A 575 LYS cc_start: 0.3156 (OUTLIER) cc_final: 0.2427 (ptpp) REVERT: A 832 ILE cc_start: 0.5269 (OUTLIER) cc_final: 0.4831 (pt) REVERT: A 974 THR cc_start: 0.3764 (OUTLIER) cc_final: 0.3401 (m) REVERT: A 1020 ASP cc_start: 0.5158 (OUTLIER) cc_final: 0.4734 (m-30) REVERT: A 1050 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8092 (tt0) REVERT: A 1270 ILE cc_start: 0.6195 (OUTLIER) cc_final: 0.5912 (pp) REVERT: A 1305 THR cc_start: 0.4045 (OUTLIER) cc_final: 0.3747 (p) REVERT: A 1310 LYS cc_start: 0.7911 (pttm) cc_final: 0.6508 (mmmt) REVERT: A 1325 LEU cc_start: 0.6461 (tp) cc_final: 0.6221 (mt) REVERT: A 1332 MET cc_start: 0.7326 (tpt) cc_final: 0.7116 (mmt) REVERT: A 1338 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5150 (pp) REVERT: A 1472 ASN cc_start: 0.6508 (OUTLIER) cc_final: 0.5885 (m-40) REVERT: A 1483 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6382 (tp) REVERT: A 1854 ILE cc_start: 0.6504 (OUTLIER) cc_final: 0.6210 (mt) REVERT: A 1930 LEU cc_start: 0.3234 (OUTLIER) cc_final: 0.2443 (tp) REVERT: A 1948 GLU cc_start: 0.1783 (OUTLIER) cc_final: 0.1436 (mp0) REVERT: A 1959 PHE cc_start: 0.4766 (OUTLIER) cc_final: 0.4398 (m-80) REVERT: A 2216 GLU cc_start: 0.3249 (OUTLIER) cc_final: 0.3021 (tm-30) REVERT: A 2269 MET cc_start: -0.0148 (tpp) cc_final: -0.1191 (tpt) REVERT: A 2274 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6638 (pp) outliers start: 181 outliers final: 87 residues processed: 304 average time/residue: 0.4296 time to fit residues: 155.5900 Evaluate side-chains 255 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 141 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLN Chi-restraints excluded: chain A residue 14 TYR Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 47 LEU 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 148 SER Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 191 LYS 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 314 MET Chi-restraints excluded: chain A residue 318 GLU 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 417 SER Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 572 THR 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 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 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 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 1164 LEU Chi-restraints excluded: chain A residue 1181 THR 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 1305 THR 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 1378 GLU Chi-restraints excluded: chain A residue 1383 ILE 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 1441 SER Chi-restraints excluded: chain A residue 1472 ASN 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 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 1644 THR Chi-restraints excluded: chain A residue 1698 LEU 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 1798 SER 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 1959 PHE 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 2127 ASP Chi-restraints excluded: chain A residue 2159 LEU 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 2274 LEU Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2354 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 215 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 221 optimal weight: 0.8980 chunk 151 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 153 optimal weight: 3.9990 chunk 220 optimal weight: 20.0000 chunk 135 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 HIS ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 ASN ** A1052 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1158 ASN ** A1590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5236 r_free = 0.5236 target = 0.248436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.208080 restraints weight = 24089.563| |-----------------------------------------------------------------------------| r_work (start): 0.4865 rms_B_bonded: 3.39 r_work: 0.4507 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19473 Z= 0.127 Angle : 0.629 9.881 26343 Z= 0.333 Chirality : 0.046 0.182 2905 Planarity : 0.004 0.057 3406 Dihedral : 7.801 59.473 2630 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.61 % Favored : 93.31 % Rotamer: Outliers : 7.11 % Allowed : 34.11 % Favored : 58.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.17), residues: 2361 helix: -0.50 (0.20), residues: 646 sheet: -1.49 (0.25), residues: 431 loop : -1.48 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2026 TYR 0.013 0.001 TYR A 690 PHE 0.036 0.002 PHE A 335 TRP 0.013 0.001 TRP A1743 HIS 0.003 0.001 HIS A1178 Details of bonding type rmsd covalent geometry : bond 0.00283 (19471) covalent geometry : angle 0.62879 (26343) hydrogen bonds : bond 0.03580 ( 714) hydrogen bonds : angle 5.30468 ( 1914) metal coordination : bond 0.00087 ( 2) *********************** 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 305 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 153 time to evaluate : 0.739 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 68 ARG cc_start: 0.5629 (OUTLIER) cc_final: 0.4640 (ptp90) REVERT: A 81 MET cc_start: 0.6192 (OUTLIER) cc_final: 0.5930 (ttt) REVERT: A 190 TYR cc_start: 0.5768 (OUTLIER) cc_final: 0.4391 (t80) REVERT: A 213 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.4183 (mp0) REVERT: A 278 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6864 (ttpt) REVERT: A 314 MET cc_start: 0.3935 (OUTLIER) cc_final: 0.3058 (mmm) REVERT: A 318 GLU cc_start: 0.4960 (OUTLIER) cc_final: 0.4153 (mp0) REVERT: A 395 CYS cc_start: 0.5700 (OUTLIER) cc_final: 0.5493 (m) REVERT: A 445 MET cc_start: 0.5736 (tpp) cc_final: 0.5295 (tmm) REVERT: A 573 ARG cc_start: 0.1802 (OUTLIER) cc_final: -0.0827 (ptt180) REVERT: A 575 LYS cc_start: 0.3009 (OUTLIER) cc_final: 0.2266 (ptpp) REVERT: A 642 ASN cc_start: 0.5605 (OUTLIER) cc_final: 0.4417 (p0) REVERT: A 727 MET cc_start: 0.5260 (tmt) cc_final: 0.4840 (pp-130) REVERT: A 806 ASN cc_start: 0.5352 (m-40) cc_final: 0.5140 (m-40) REVERT: A 832 ILE cc_start: 0.5104 (OUTLIER) cc_final: 0.4742 (pt) REVERT: A 974 THR cc_start: 0.3494 (OUTLIER) cc_final: 0.3240 (m) REVERT: A 1020 ASP cc_start: 0.5056 (OUTLIER) cc_final: 0.4649 (m-30) REVERT: A 1050 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7985 (tt0) REVERT: A 1270 ILE cc_start: 0.6068 (OUTLIER) cc_final: 0.5812 (pp) REVERT: A 1305 THR cc_start: 0.3825 (OUTLIER) cc_final: 0.3521 (p) REVERT: A 1310 LYS cc_start: 0.7754 (pttm) cc_final: 0.6355 (mmpt) REVERT: A 1325 LEU cc_start: 0.6589 (tp) cc_final: 0.6331 (mt) REVERT: A 1332 MET cc_start: 0.7320 (tpt) cc_final: 0.7022 (mmt) REVERT: A 1338 LEU cc_start: 0.6129 (OUTLIER) cc_final: 0.5267 (pp) REVERT: A 1483 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6564 (tp) REVERT: A 1613 ILE cc_start: 0.6724 (OUTLIER) cc_final: 0.6398 (mm) REVERT: A 1798 SER cc_start: 0.6543 (OUTLIER) cc_final: 0.6199 (p) REVERT: A 1948 GLU cc_start: 0.1596 (OUTLIER) cc_final: 0.1302 (mp0) REVERT: A 1959 PHE cc_start: 0.4486 (OUTLIER) cc_final: 0.4201 (m-80) REVERT: A 2269 MET cc_start: -0.0283 (tpp) cc_final: -0.1211 (tpt) REVERT: A 2274 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6757 (pp) REVERT: A 2298 ASP cc_start: 0.0196 (OUTLIER) cc_final: -0.0238 (p0) REVERT: A 2312 ASN cc_start: 0.4359 (OUTLIER) cc_final: 0.4115 (p0) outliers start: 152 outliers final: 81 residues processed: 285 average time/residue: 0.4365 time to fit residues: 147.7406 Evaluate side-chains 248 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 142 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 148 SER 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 260 VAL Chi-restraints excluded: chain A residue 278 LYS 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 395 CYS Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 572 THR 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 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 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 887 GLU 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 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 1181 THR Chi-restraints excluded: chain A residue 1187 PHE Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1236 TRP Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1305 THR 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 1400 ARG 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 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 1641 ILE Chi-restraints excluded: chain A residue 1644 THR 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 1798 SER Chi-restraints excluded: chain A residue 1857 PHE 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 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 2127 ASP Chi-restraints excluded: chain A residue 2159 LEU 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 2273 TYR Chi-restraints excluded: chain A residue 2274 LEU Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2298 ASP 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 184 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 209 optimal weight: 20.0000 chunk 174 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 222 optimal weight: 20.0000 chunk 40 optimal weight: 0.6980 chunk 185 optimal weight: 0.6980 chunk 144 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 154 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN A 58 ASN ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 ASN 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 = 0.5240 r_free = 0.5240 target = 0.249194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.209865 restraints weight = 24180.647| |-----------------------------------------------------------------------------| r_work (start): 0.4882 rms_B_bonded: 3.58 r_work: 0.4503 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19473 Z= 0.122 Angle : 0.634 14.977 26343 Z= 0.332 Chirality : 0.046 0.202 2905 Planarity : 0.004 0.057 3406 Dihedral : 7.546 59.131 2622 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.65 % Favored : 93.27 % Rotamer: Outliers : 6.27 % Allowed : 35.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.17), residues: 2361 helix: -0.28 (0.20), residues: 644 sheet: -1.28 (0.25), residues: 410 loop : -1.40 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A2026 TYR 0.023 0.001 TYR A1323 PHE 0.033 0.002 PHE A1269 TRP 0.012 0.001 TRP A1743 HIS 0.002 0.001 HIS A1257 Details of bonding type rmsd covalent geometry : bond 0.00271 (19471) covalent geometry : angle 0.63354 (26343) hydrogen bonds : bond 0.03464 ( 714) hydrogen bonds : angle 5.18544 ( 1914) metal coordination : bond 0.00073 ( 2) *********************** 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 287 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 153 time to evaluate : 0.808 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 17 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.6751 (m-80) REVERT: A 68 ARG cc_start: 0.5647 (OUTLIER) cc_final: 0.4762 (ptp90) REVERT: A 81 MET cc_start: 0.6215 (OUTLIER) cc_final: 0.5903 (ttt) REVERT: A 190 TYR cc_start: 0.5800 (OUTLIER) cc_final: 0.4749 (t80) REVERT: A 191 LYS cc_start: 0.6947 (mttm) cc_final: 0.6588 (mttm) REVERT: A 213 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.4284 (mp0) REVERT: A 278 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6859 (ttpt) REVERT: A 318 GLU cc_start: 0.5008 (OUTLIER) cc_final: 0.4280 (mp0) REVERT: A 321 MET cc_start: 0.4809 (tpp) cc_final: 0.4177 (tpt) REVERT: A 395 CYS cc_start: 0.5548 (OUTLIER) cc_final: 0.5274 (m) REVERT: A 445 MET cc_start: 0.5744 (tpp) cc_final: 0.5296 (tmm) REVERT: A 573 ARG cc_start: 0.1969 (OUTLIER) cc_final: -0.0541 (ptt180) REVERT: A 575 LYS cc_start: 0.2846 (OUTLIER) cc_final: 0.2151 (ptpp) REVERT: A 634 TYR cc_start: 0.3296 (m-80) cc_final: 0.1950 (m-80) REVERT: A 640 ILE cc_start: -0.0127 (OUTLIER) cc_final: -0.0332 (mt) REVERT: A 690 TYR cc_start: 0.4133 (OUTLIER) cc_final: 0.2037 (t80) REVERT: A 832 ILE cc_start: 0.5035 (OUTLIER) cc_final: 0.4682 (pt) REVERT: A 974 THR cc_start: 0.3654 (OUTLIER) cc_final: 0.3422 (m) REVERT: A 1020 ASP cc_start: 0.5099 (OUTLIER) cc_final: 0.4694 (m-30) REVERT: A 1050 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7989 (tt0) REVERT: A 1310 LYS cc_start: 0.7709 (pttm) cc_final: 0.7446 (pmtt) REVERT: A 1325 LEU cc_start: 0.6670 (tp) cc_final: 0.6383 (mt) REVERT: A 1338 LEU cc_start: 0.5891 (OUTLIER) cc_final: 0.5192 (pp) REVERT: A 1483 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6720 (tp) REVERT: A 1530 ASN cc_start: 0.7289 (OUTLIER) cc_final: 0.6949 (p0) REVERT: A 1613 ILE cc_start: 0.6776 (OUTLIER) cc_final: 0.6274 (tp) REVERT: A 1702 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.5614 (tp30) REVERT: A 1798 SER cc_start: 0.6583 (OUTLIER) cc_final: 0.6222 (p) REVERT: A 1948 GLU cc_start: 0.1593 (OUTLIER) cc_final: 0.1308 (mp0) REVERT: A 1959 PHE cc_start: 0.4550 (OUTLIER) cc_final: 0.4236 (m-80) REVERT: A 2269 MET cc_start: -0.0313 (tpp) cc_final: -0.1220 (tpt) REVERT: A 2274 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6767 (pp) REVERT: A 2298 ASP cc_start: 0.0364 (OUTLIER) cc_final: -0.0089 (p0) REVERT: A 2312 ASN cc_start: 0.4528 (OUTLIER) cc_final: 0.4219 (p0) outliers start: 134 outliers final: 78 residues processed: 273 average time/residue: 0.4496 time to fit residues: 145.6857 Evaluate side-chains 246 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 142 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLN Chi-restraints excluded: chain A residue 17 PHE 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 148 SER Chi-restraints excluded: chain A residue 190 TYR 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 278 LYS 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 395 CYS Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 572 THR 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 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 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 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 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 1181 THR Chi-restraints excluded: chain A residue 1187 PHE Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1236 TRP 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 1512 ASP 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 1641 ILE Chi-restraints excluded: chain A residue 1644 THR 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 1748 SER Chi-restraints excluded: chain A residue 1798 SER 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 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 2127 ASP Chi-restraints excluded: chain A residue 2159 LEU 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 2273 TYR Chi-restraints excluded: chain A residue 2274 LEU Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2298 ASP Chi-restraints excluded: chain A residue 2306 GLN 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 117 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 130 optimal weight: 0.0870 chunk 163 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 211 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- 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 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 402 GLN A 659 ASN A1052 ASN A1158 ASN A1663 HIS ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2148 ASN ** A2270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5231 r_free = 0.5231 target = 0.248203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.208349 restraints weight = 24026.289| |-----------------------------------------------------------------------------| r_work (start): 0.4867 rms_B_bonded: 3.57 r_work: 0.4491 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19473 Z= 0.131 Angle : 0.642 13.428 26343 Z= 0.337 Chirality : 0.046 0.193 2905 Planarity : 0.004 0.056 3406 Dihedral : 7.518 59.783 2618 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.95 % Favored : 92.97 % Rotamer: Outliers : 6.41 % Allowed : 35.28 % Favored : 58.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.17), residues: 2361 helix: -0.33 (0.20), residues: 643 sheet: -1.30 (0.25), residues: 421 loop : -1.38 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2026 TYR 0.021 0.001 TYR A1323 PHE 0.041 0.002 PHE A 335 TRP 0.011 0.001 TRP A1743 HIS 0.002 0.001 HIS A1178 Details of bonding type rmsd covalent geometry : bond 0.00291 (19471) covalent geometry : angle 0.64159 (26343) hydrogen bonds : bond 0.03574 ( 714) hydrogen bonds : angle 5.21940 ( 1914) metal coordination : bond 0.00089 ( 2) *********************** 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 281 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 144 time to evaluate : 0.755 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 17 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.6775 (m-80) REVERT: A 68 ARG cc_start: 0.5668 (OUTLIER) cc_final: 0.4856 (mtm180) REVERT: A 81 MET cc_start: 0.6197 (OUTLIER) cc_final: 0.5892 (ttt) REVERT: A 190 TYR cc_start: 0.5681 (OUTLIER) cc_final: 0.4557 (t80) REVERT: A 191 LYS cc_start: 0.6822 (mttm) cc_final: 0.6520 (mttm) REVERT: A 213 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.4345 (mp0) REVERT: A 278 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6845 (ttpt) REVERT: A 314 MET cc_start: 0.4033 (OUTLIER) cc_final: 0.3124 (mmm) REVERT: A 321 MET cc_start: 0.4783 (tpp) cc_final: 0.4122 (tpt) REVERT: A 395 CYS cc_start: 0.5726 (OUTLIER) cc_final: 0.5474 (m) REVERT: A 402 GLN cc_start: 0.6381 (OUTLIER) cc_final: 0.6102 (tp40) REVERT: A 445 MET cc_start: 0.5784 (tpp) cc_final: 0.5308 (tmm) REVERT: A 573 ARG cc_start: 0.1904 (OUTLIER) cc_final: -0.0558 (ptt180) REVERT: A 575 LYS cc_start: 0.2680 (OUTLIER) cc_final: 0.1954 (ptpp) REVERT: A 640 ILE cc_start: -0.0165 (OUTLIER) cc_final: -0.0371 (mt) REVERT: A 690 TYR cc_start: 0.4230 (OUTLIER) cc_final: 0.2066 (t80) REVERT: A 832 ILE cc_start: 0.5061 (OUTLIER) cc_final: 0.4717 (pt) REVERT: A 974 THR cc_start: 0.3734 (OUTLIER) cc_final: 0.3447 (m) REVERT: A 1020 ASP cc_start: 0.5004 (OUTLIER) cc_final: 0.4581 (m-30) REVERT: A 1050 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7946 (tt0) REVERT: A 1310 LYS cc_start: 0.7703 (pttm) cc_final: 0.7450 (pmtt) REVERT: A 1325 LEU cc_start: 0.6668 (tp) cc_final: 0.6382 (mt) REVERT: A 1338 LEU cc_start: 0.5944 (OUTLIER) cc_final: 0.5340 (pp) REVERT: A 1530 ASN cc_start: 0.7332 (OUTLIER) cc_final: 0.7016 (p0) REVERT: A 1613 ILE cc_start: 0.6742 (OUTLIER) cc_final: 0.6241 (tp) REVERT: A 1702 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.5648 (tp30) REVERT: A 1798 SER cc_start: 0.6592 (OUTLIER) cc_final: 0.6245 (p) REVERT: A 1854 ILE cc_start: 0.6428 (OUTLIER) cc_final: 0.6152 (mt) REVERT: A 1930 LEU cc_start: 0.3188 (OUTLIER) cc_final: 0.2474 (tp) REVERT: A 1959 PHE cc_start: 0.4480 (OUTLIER) cc_final: 0.4146 (m-80) REVERT: A 2269 MET cc_start: -0.0327 (tpp) cc_final: -0.1235 (tpt) REVERT: A 2274 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6780 (pp) REVERT: A 2298 ASP cc_start: 0.0341 (OUTLIER) cc_final: -0.0108 (p0) REVERT: A 2312 ASN cc_start: 0.4434 (OUTLIER) cc_final: 0.4176 (p0) outliers start: 137 outliers final: 84 residues processed: 265 average time/residue: 0.4173 time to fit residues: 132.4150 Evaluate side-chains 252 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 141 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLN Chi-restraints excluded: chain A residue 17 PHE 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 148 SER 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 260 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 307 ILE 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 365 ASP 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 417 SER Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 572 THR 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 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 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 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 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 1181 THR Chi-restraints excluded: chain A residue 1187 PHE Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1236 TRP Chi-restraints excluded: chain A residue 1248 THR 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 1485 THR Chi-restraints excluded: chain A residue 1512 ASP 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 1644 THR Chi-restraints excluded: chain A residue 1685 ILE 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 1748 SER Chi-restraints excluded: chain A residue 1798 SER 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 1959 PHE Chi-restraints excluded: chain A residue 2008 VAL Chi-restraints excluded: chain A residue 2104 VAL Chi-restraints excluded: chain A residue 2120 LEU Chi-restraints excluded: chain A residue 2127 ASP Chi-restraints excluded: chain A residue 2159 LEU 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 2273 TYR Chi-restraints excluded: chain A residue 2274 LEU Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2298 ASP 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 135 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 62 optimal weight: 0.0870 chunk 134 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 185 optimal weight: 0.3980 chunk 173 optimal weight: 2.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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 343 GLN A 659 ASN A1052 ASN A1158 ASN A1663 HIS ** A1851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2007 GLN ** 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 = 0.5239 r_free = 0.5239 target = 0.249015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.209469 restraints weight = 24234.573| |-----------------------------------------------------------------------------| r_work (start): 0.4875 rms_B_bonded: 3.38 r_work: 0.4506 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19473 Z= 0.125 Angle : 0.644 13.142 26343 Z= 0.337 Chirality : 0.046 0.192 2905 Planarity : 0.004 0.056 3406 Dihedral : 7.340 57.984 2612 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.65 % Favored : 93.27 % Rotamer: Outliers : 5.47 % Allowed : 36.13 % Favored : 58.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.17), residues: 2361 helix: -0.20 (0.20), residues: 637 sheet: -1.24 (0.25), residues: 421 loop : -1.35 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2026 TYR 0.018 0.001 TYR A1477 PHE 0.036 0.002 PHE A2031 TRP 0.011 0.001 TRP A1743 HIS 0.003 0.001 HIS A1186 Details of bonding type rmsd covalent geometry : bond 0.00282 (19471) covalent geometry : angle 0.64396 (26343) hydrogen bonds : bond 0.03480 ( 714) hydrogen bonds : angle 5.18192 ( 1914) metal coordination : bond 0.00090 ( 2) ********************** 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: 117 poor density : 146 time to evaluate : 0.726 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 17 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.6799 (m-80) REVERT: A 68 ARG cc_start: 0.5639 (OUTLIER) cc_final: 0.4576 (ptp-170) REVERT: A 81 MET cc_start: 0.6259 (OUTLIER) cc_final: 0.5942 (ttt) REVERT: A 190 TYR cc_start: 0.5656 (OUTLIER) cc_final: 0.4654 (t80) REVERT: A 191 LYS cc_start: 0.6816 (mttm) cc_final: 0.6413 (mttm) REVERT: A 213 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.4393 (mp0) REVERT: A 314 MET cc_start: 0.3954 (OUTLIER) cc_final: 0.3099 (mmm) REVERT: A 321 MET cc_start: 0.4859 (tpp) cc_final: 0.4351 (tpt) REVERT: A 445 MET cc_start: 0.5782 (tpp) cc_final: 0.5313 (tmm) REVERT: A 573 ARG cc_start: 0.1840 (OUTLIER) cc_final: -0.0760 (ptt180) REVERT: A 575 LYS cc_start: 0.2694 (OUTLIER) cc_final: 0.1979 (ptpp) REVERT: A 634 TYR cc_start: 0.3362 (m-80) cc_final: 0.2010 (m-80) REVERT: A 690 TYR cc_start: 0.4331 (OUTLIER) cc_final: 0.2210 (t80) REVERT: A 727 MET cc_start: 0.6149 (ppp) cc_final: 0.5913 (ppp) REVERT: A 832 ILE cc_start: 0.5016 (OUTLIER) cc_final: 0.4662 (pt) REVERT: A 920 GLU cc_start: 0.6255 (tp30) cc_final: 0.5979 (tm-30) REVERT: A 974 THR cc_start: 0.3510 (OUTLIER) cc_final: 0.3236 (m) REVERT: A 1020 ASP cc_start: 0.5023 (OUTLIER) cc_final: 0.4609 (m-30) REVERT: A 1050 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7940 (tt0) REVERT: A 1325 LEU cc_start: 0.6616 (tp) cc_final: 0.6339 (mt) REVERT: A 1338 LEU cc_start: 0.5830 (OUTLIER) cc_final: 0.5312 (pp) REVERT: A 1613 ILE cc_start: 0.6750 (OUTLIER) cc_final: 0.6254 (tp) REVERT: A 1698 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6389 (mt) REVERT: A 1702 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6344 (mt-10) REVERT: A 1798 SER cc_start: 0.6585 (OUTLIER) cc_final: 0.6243 (p) REVERT: A 1854 ILE cc_start: 0.6412 (OUTLIER) cc_final: 0.6147 (mt) REVERT: A 1959 PHE cc_start: 0.4380 (OUTLIER) cc_final: 0.4094 (m-80) REVERT: A 2269 MET cc_start: -0.0317 (tpp) cc_final: -0.1226 (tpt) REVERT: A 2274 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6830 (pp) REVERT: A 2298 ASP cc_start: 0.0173 (OUTLIER) cc_final: -0.0252 (p0) REVERT: A 2312 ASN cc_start: 0.4357 (OUTLIER) cc_final: 0.4112 (p0) outliers start: 117 outliers final: 81 residues processed: 252 average time/residue: 0.4244 time to fit residues: 127.9623 Evaluate side-chains 242 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 139 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE 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 148 SER Chi-restraints excluded: chain A residue 190 TYR 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 307 ILE Chi-restraints excluded: chain A residue 314 MET 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 395 CYS Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 572 THR 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 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 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 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 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 1181 THR Chi-restraints excluded: chain A residue 1187 PHE Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1236 TRP Chi-restraints excluded: chain A residue 1248 THR 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 1441 SER Chi-restraints excluded: chain A residue 1512 ASP 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 1641 ILE Chi-restraints excluded: chain A residue 1644 THR Chi-restraints excluded: chain A residue 1685 ILE 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 1798 SER 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 1959 PHE Chi-restraints excluded: chain A residue 2008 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 2127 ASP Chi-restraints excluded: chain A residue 2159 LEU 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 2273 TYR Chi-restraints excluded: chain A residue 2274 LEU Chi-restraints excluded: chain A residue 2296 THR Chi-restraints excluded: chain A residue 2298 ASP Chi-restraints excluded: chain A residue 2306 GLN 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 188 optimal weight: 0.0470 chunk 124 optimal weight: 7.9990 chunk 192 optimal weight: 0.0980 chunk 132 optimal weight: 4.9990 chunk 53 optimal weight: 0.2980 chunk 212 optimal weight: 0.9990 chunk 135 optimal weight: 0.1980 chunk 98 optimal weight: 0.5980 chunk 218 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.2478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 ASN A 659 ASN A 835 GLN A1052 ASN A1158 ASN A1663 HIS ** 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 = 0.5279 r_free = 0.5279 target = 0.252699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4954 r_free = 0.4954 target = 0.214497 restraints weight = 24115.671| |-----------------------------------------------------------------------------| r_work (start): 0.4930 rms_B_bonded: 3.26 r_work: 0.4569 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5962 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 19473 Z= 0.107 Angle : 0.606 13.783 26343 Z= 0.317 Chirality : 0.045 0.188 2905 Planarity : 0.004 0.059 3406 Dihedral : 6.696 59.481 2602 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.06 % Favored : 93.86 % Rotamer: Outliers : 4.26 % Allowed : 37.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.17), residues: 2361 helix: 0.13 (0.21), residues: 637 sheet: -1.13 (0.26), residues: 418 loop : -1.23 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2026 TYR 0.019 0.001 TYR A1477 PHE 0.038 0.001 PHE A 335 TRP 0.013 0.001 TRP A1743 HIS 0.003 0.001 HIS A1186 Details of bonding type rmsd covalent geometry : bond 0.00234 (19471) covalent geometry : angle 0.60611 (26343) hydrogen bonds : bond 0.02998 ( 714) hydrogen bonds : angle 4.94525 ( 1914) metal coordination : bond 0.00020 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7909.30 seconds wall clock time: 135 minutes 19.07 seconds (8119.07 seconds total)